rs10213926

Positions:

• chr5-9482435-G-A

Variant summary

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

The NM_003966.3(SEMA5A):​c.-174-44583C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0769 in 152,156 control chromosomes in the GnomAD database, including 489 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 0.077 (489 hom., cov: 33)
• Consequence: SEMA5A NM_003966.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

Genes affected

SEMA5A (HGNC:10736): (semaphorin 5A) This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene.[provided by RefSeq, Jan 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEMA5A	NM_003966.3	c.-174-44583C>T		intron_variant		ENST00000382496.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEMA5A	ENST00000382496.10	c.-174-44583C>T		intron_variant		1	NM_003966.3	P1
SEMA5A	ENST00000652226.1	c.-392-44583C>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11668 AN: 152040 Hom.: 482 Cov.: 33

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.0420

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0769 AC: 11699 AN: 152156 Hom.: 489 Cov.: 33 AF XY: 0.0772 AC XY: 5740 AN XY: 74394

Gnomad4 AFR AF: 0.0699

Gnomad4 AMR AF: 0.0723

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.0419

Gnomad4 SAS AF: 0.0994

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.0818

Gnomad4 OTH AF: 0.0785

Alfa AF: 0.0794 Hom.: 78

Bravo AF: 0.0715

Asia WGS AF: 0.129 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.35

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: rs10213926; hg19: chr5-9482547;