rs56131427

Variant names:

• chr7-85055645-CATATATATATATATATATATATATATATAT-C
• rs56131427
• NM_001384900.1:c.861+42_861+71delATATATATATATATATATATATATATATAT

Your query was ambiguous. Multiple possible variants found:

• chr7-85055645-CATATATATATATATATATATATATATATAT-C
• chr7-85055645-CATATATATATATATATATATATATATATAT-CAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATATATATATATATATATAT
• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATATATATATATATATATATATATATATAT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001384900.1(SEMA3D):​c.861+42_861+71delATATATATATATATATATATATATATATAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000375 in 159,812 control chromosomes in the GnomAD database, including 2 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000036 (1 hom., cov: 0)
  • Exomes 𝑓: 0.000042 (1 hom.)
• Consequence: SEMA3D NM_001384900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.718
• Publications: 1 publications found

Genes affected

SEMA3D (HGNC:10726): (semaphorin 3D) This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA3D	NM_001384900.1	c.861+42_861+71delATATATATATATATATATATATATATATAT		intron_variant	Intron 9 of 18	ENST00000284136.11	NP_001371829.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEMA3D	ENST00000284136.11	c.861+42_861+71delATATATATATATATATATATATATATATAT		intron_variant	Intron 9 of 18	5	NM_001384900.1	ENSP00000284136.6
SEMA3D	ENST00000444867.1	c.861+42_861+71delATATATATATATATATATATATATATATAT		intron_variant	Intron 9 of 9	1		ENSP00000401366.1
SEMA3D	ENST00000463315.1	n.49+42_49+71delATATATATATATATATATATATATATATAT		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0000358 AC: 4 AN: 111640 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.0000989

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000687

GnomAD4 exome AF: 0.0000415 AC: 2 AN: 48170 Hom.: 1 AF XY: 0.0000719 AC XY: 2 AN XY: 27810

African (AFR) AF: 0.00 AC: 0 AN: 690

American (AMR) AF: 0.00 AC: 0 AN: 774

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 712

East Asian (EAS) AF: 0.00 AC: 0 AN: 1038

South Asian (SAS) AF: 0.00195 AC: 2 AN: 1024

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1262

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 118

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 40692

Other (OTH) AF: 0.00 AC: 0 AN: 1860

GnomAD4 genome AF: 0.0000358 AC: 4 AN: 111642 Hom.: 1 Cov.: 0 AF XY: 0.0000193 AC XY: 1 AN XY: 51824

African (AFR) AF: 0.0000987 AC: 3 AN: 30380

American (AMR) AF: 0.00 AC: 0 AN: 9572

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2948

East Asian (EAS) AF: 0.00 AC: 0 AN: 3598

South Asian (SAS) AF: 0.00 AC: 0 AN: 2992

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3644

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 200

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 56062

Other (OTH) AF: 0.000681 AC: 1 AN: 1468

Alfa AF: 0.00 Hom.: 173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs56131427; hg19: chr7-84684961;