chr5-9332169-T-A

Position:

• chr5-9332169-T-A

Variant summary

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

The NM_003966.3(SEMA5A):​c.224+5544A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 151,576 control chromosomes in the GnomAD database, including 40,229 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 0.71 (40229 hom., cov: 31)
• Consequence: SEMA5A NM_003966.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

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 (NFE) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEMA5A	NM_003966.3	c.224+5544A>T		intron_variant		ENST00000382496.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEMA5A	ENST00000382496.10	c.224+5544A>T		intron_variant		1	NM_003966.3	P1
SEMA5A	ENST00000513968.4	c.224+5544A>T		intron_variant		5
SEMA5A	ENST00000652226.1	c.224+5544A>T		intron_variant				P1
SEMA5A	ENST00000509486.2	n.301+5544A>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.706 AC: 106961 AN: 151460 Hom.: 40232 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.706 AC: 106986 AN: 151576 Hom.: 40229 Cov.: 31 AF XY: 0.706 AC XY: 52296 AN XY: 74084

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.745

Alfa AF: 0.815 Hom.: 28296

Bravo AF: 0.682

Asia WGS AF: 0.713 AC: 2481 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	3.2
DANN	Benign	0.58

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: rs7702187; hg19: chr5-9332281;