rs9313272

Variant names:

• chr5-9321453-T-A
• rs9313272
• NM_003966.3:c.225-3036A>T

Variant summary

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

The NM_003966.3(SEMA5A):​c.225-3036A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,162 control chromosomes in the GnomAD database, including 2,695 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 0.17 (2695 hom., cov: 32)
• Consequence: SEMA5A NM_003966.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA5A	NM_003966.3	c.225-3036A>T		intron_variant	Intron 4 of 22	ENST00000382496.10	NP_003957.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEMA5A	ENST00000382496.10	c.225-3036A>T		intron_variant	Intron 4 of 22	1	NM_003966.3	ENSP00000371936.5
SEMA5A	ENST00000652226.1	c.225-3036A>T		intron_variant	Intron 6 of 24			ENSP00000499013.1
SEMA5A	ENST00000513968.4	c.225-3036A>T		intron_variant	Intron 3 of 7	5		ENSP00000421961.1
SEMA5A	ENST00000509486.2	n.302-3036A>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25672 AN: 152044 Hom.: 2692 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.169 AC: 25673 AN: 152162 Hom.: 2695 Cov.: 32 AF XY: 0.170 AC XY: 12627 AN XY: 74368

African (AFR) AF: 0.0443 AC: 1842 AN: 41542

American (AMR) AF: 0.174 AC: 2662 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3470

East Asian (EAS) AF: 0.130 AC: 674 AN: 5170

South Asian (SAS) AF: 0.231 AC: 1115 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2689 AN: 10582

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15370 AN: 67990

Other (OTH) AF: 0.165 AC: 349 AN: 2110

Alfa AF: 0.204 Hom.: 502

Bravo AF: 0.154

Asia WGS AF: 0.162 AC: 565 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	1.1
DANN	Benign	0.73
PhyloP100		-0.097
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9313272; hg19: chr5-9321565;