rs4603502

chr15-47582457-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558014.5(SEMA6D):c.-86-18408T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,148 control chromosomes in the GnomAD database, including 5,693 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 0.26 (5693 hom., cov: 32)
• Consequence: SEMA6D ENST00000558014.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEMA6D	NM_001198999.2	c.-86-18408T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEMA6D	ENST00000558014.5	c.-86-18408T>C		intron_variant		1		A1
SEMA6D	ENST00000559184.5	c.-86-18408T>C		intron_variant		4
SEMA6D	ENST00000560636.5	c.-170-18408T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38871 AN: 152030 Hom.: 5683 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.256 AC: 38892 AN: 152148 Hom.: 5693 Cov.: 32 AF XY: 0.254 AC XY: 18879 AN XY: 74350

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.298

Alfa AF: 0.288 Hom.: 3272

Bravo AF: 0.264

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	8.6
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4603502; hg19: chr15-47874654;