rs649483

chr15-47349702-A-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000558014.5(SEMA6D):c.-238-62691A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,090 control chromosomes in the GnomAD database, including 19,714 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 0.47 (19714 hom., cov: 33)
• Consequence: SEMA6D ENST00000558014.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73

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]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEMA6D	NM_001198999.2	c.-238-62691A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEMA6D	ENST00000558014.5	c.-238-62691A>G		intron_variant		1		A1
SEMA6D	ENST00000559184.5	c.-238-62691A>G		intron_variant		4
SEMA6D	ENST00000560636.5	c.-323+10483A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71064 AN: 151972 Hom.: 19731 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.467 AC: 71040 AN: 152090 Hom.: 19714 Cov.: 33 AF XY: 0.475 AC XY: 35338 AN XY: 74346

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.490

Alfa AF: 0.544 Hom.: 3121

Bravo AF: 0.440

Asia WGS AF: 0.452 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
Cadd	Benign	19
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs649483; hg19: chr15-47641899;