7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATAT

Position:

• chr7-85055645-CATATATATATATATATATATATATATATAT-CATATATATATATATATATATATATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001384900.1(SEMA3D):​c.861+68_861+71delATAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0521 in 159,060 control chromosomes in the GnomAD database, including 248 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.067 (247 hom., cov: 0)
  • Exomes 𝑓: 0.018 (1 hom.)
• Consequence: SEMA3D NM_001384900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEMA3D	NM_001384900.1	c.861+68_861+71delATAT		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+68_861+71delATAT		intron_variant		5	NM_001384900.1	ENSP00000284136.6
SEMA3D	ENST00000444867.1	c.861+68_861+71delATAT		intron_variant		1		ENSP00000401366.1
SEMA3D	ENST00000463315.1	n.49+68_49+71delATAT		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 7435 AN: 111262 Hom.: 247 Cov.: 0

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.0180

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.0631

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.0591

GnomAD4 exome AF: 0.0179 AC: 854 AN: 47796 Hom.: 1 AF XY: 0.0192 AC XY: 529 AN XY: 27588

Gnomad4 AFR exome AF: 0.0205

Gnomad4 AMR exome AF: 0.0313

Gnomad4 ASJ exome AF: 0.0226

Gnomad4 EAS exome AF: 0.0489

Gnomad4 SAS exome AF: 0.0287

Gnomad4 FIN exome AF: 0.0319

Gnomad4 NFE exome AF: 0.0158

Gnomad4 OTH exome AF: 0.0216

GnomAD4 genome AF: 0.0669 AC: 7438 AN: 111264 Hom.: 247 Cov.: 0 AF XY: 0.0667 AC XY: 3442 AN XY: 51636

Gnomad4 AFR AF: 0.0632

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0522

Gnomad4 NFE AF: 0.0602

Gnomad4 OTH AF: 0.0587

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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;