7-85055645-CATATATATATATATATATATATATATATAT-CATATATATAT

Position:

• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATAT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001384900.1(SEMA3D):​c.861+52_861+71delATATATATATATATATATAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00236 in 159,482 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00069 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0063 (1 hom.)
• Consequence: SEMA3D NM_001384900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.718

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]

SEMA3D (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEMA3D	NM_001384900.1	c.861+52_861+71delATATATATATATATATATAT		intron_variant		ENST00000284136.11	NP_001371829.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEMA3D	ENST00000284136.11	c.861+52_861+71delATATATATATATATATATAT		intron_variant		5	NM_001384900.1	ENSP00000284136.6
SEMA3D	ENST00000444867.1	c.861+52_861+71delATATATATATATATATATAT		intron_variant		1		ENSP00000401366.1
SEMA3D	ENST00000463315.1	n.49+52_49+71delATATATATATATATATATAT		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.000663 AC: 74 AN: 111640 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00158

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000313

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000829

Gnomad SAS AF: 0.000999

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000268

Gnomad OTH AF: 0.00137

GnomAD4 exome AF: 0.00627 AC: 300 AN: 47840 Hom.: 1 AF XY: 0.00634 AC XY: 175 AN XY: 27604

Gnomad4 AFR exome AF: 0.0117

Gnomad4 AMR exome AF: 0.00391

Gnomad4 ASJ exome AF: 0.00712

Gnomad4 EAS exome AF: 0.000965

Gnomad4 SAS exome AF: 0.00491

Gnomad4 FIN exome AF: 0.00879

Gnomad4 NFE exome AF: 0.00626

Gnomad4 OTH exome AF: 0.00756

GnomAD4 genome AF: 0.000690 AC: 77 AN: 111642 Hom.: 2 Cov.: 0 AF XY: 0.000791 AC XY: 41 AN XY: 51824

Gnomad4 AFR AF: 0.00165

Gnomad4 AMR AF: 0.000313

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000834

Gnomad4 SAS AF: 0.00100

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000268

Gnomad4 OTH AF: 0.00204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56131427; hg19: chr7-84684961;