chr15-47426455-A-G

Variant names:

• chr15-47426455-A-G
• rs10467913
• ENST00000558014.5:c.-159+13983A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558014.5(SEMA6D):​c.-159+13983A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,044 control chromosomes in the GnomAD database, including 3,384 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 0.20 (3384 hom., cov: 32)
• Consequence: SEMA6D ENST00000558014.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 1 publications found

Genes affected

SEMA6D (HGNC:16770): (semaphorin 6D) Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]

SEMA6D Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA6D	NM_001198999.2	c.-159+13983A>G		intron_variant	Intron 2 of 19		NP_001185928.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEMA6D	ENST00000558014.5	c.-159+13983A>G		intron_variant	Intron 2 of 19	1		ENSP00000452815.1
SEMA6D	ENST00000559184.5	c.-159+13983A>G		intron_variant	Intron 3 of 5	4		ENSP00000453097.1
SEMA6D	ENST00000560636.5	c.-243+13983A>G		intron_variant	Intron 2 of 5	4		ENSP00000453420.1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30612 AN: 151926 Hom.: 3387 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.201 AC: 30618 AN: 152044 Hom.: 3384 Cov.: 32 AF XY: 0.208 AC XY: 15455 AN XY: 74310

African (AFR) AF: 0.118 AC: 4910 AN: 41500

American (AMR) AF: 0.172 AC: 2633 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1293 AN: 5148

South Asian (SAS) AF: 0.366 AC: 1759 AN: 4810

European-Finnish (FIN) AF: 0.288 AC: 3037 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15529 AN: 67968

Other (OTH) AF: 0.200 AC: 421 AN: 2108

Alfa AF: 0.198 Hom.: 568

Bravo AF: 0.188

Asia WGS AF: 0.258 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.5
DANN	Benign	0.68
PhyloP100		0.68
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10467913; hg19: chr15-47718652;