NM_001384900.1:c.152-10402C>T

Variant names:

• chr7-85108367-G-A
• rs10486848
• NM_001384900.1:c.152-10402C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001384900.1(SEMA3D):​c.152-10402C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,952 control chromosomes in the GnomAD database, including 1,707 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1707 hom., cov: 32)
• Consequence: SEMA3D NM_001384900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457
• Publications: 7 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: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA3D	NM_001384900.1	c.152-10402C>T		intron_variant	Intron 3 of 18	ENST00000284136.11	NP_001371829.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEMA3D	ENST00000284136.11	c.152-10402C>T		intron_variant	Intron 3 of 18	5	NM_001384900.1	ENSP00000284136.6
SEMA3D	ENST00000444867.1	c.152-10402C>T		intron_variant	Intron 3 of 9	1		ENSP00000401366.1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20356 AN: 151834 Hom.: 1705 Cov.: 32

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0651

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.143

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.134 AC: 20350 AN: 151952 Hom.: 1707 Cov.: 32 AF XY: 0.132 AC XY: 9771 AN XY: 74270

African (AFR) AF: 0.0427 AC: 1770 AN: 41480

American (AMR) AF: 0.126 AC: 1924 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3466

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5162

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4820

European-Finnish (FIN) AF: 0.181 AC: 1918 AN: 10584

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13475 AN: 67902

Other (OTH) AF: 0.141 AC: 297 AN: 2108

Alfa AF: 0.171 Hom.: 4179

Bravo AF: 0.126

Asia WGS AF: 0.0320 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	10
DANN	Benign	0.74
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10486848; hg19: chr7-84737683;