rs3797980

Variant names:

• chr5-9328204-G-A
• rs3797980
• NM_003966.3:c.224+9509C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-9328204-G-A
• chr5-9328204-G-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.224+9509C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,974 control chromosomes in the GnomAD database, including 2,325 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 0.16 (2325 hom., cov: 32)
• Consequence: SEMA5A NM_003966.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA5A	NM_003966.3	c.224+9509C>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.224+9509C>T		intron_variant	Intron 4 of 22	1	NM_003966.3	ENSP00000371936.5
SEMA5A	ENST00000652226.1	c.224+9509C>T		intron_variant	Intron 6 of 24			ENSP00000499013.1
SEMA5A	ENST00000513968.4	c.224+9509C>T		intron_variant	Intron 3 of 7	5		ENSP00000421961.1
SEMA5A	ENST00000509486.2	n.301+9509C>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24683 AN: 151856 Hom.: 2308 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0779

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.163 AC: 24753 AN: 151974 Hom.: 2325 Cov.: 32 AF XY: 0.162 AC XY: 12058 AN XY: 74282

African (AFR) AF: 0.251 AC: 10399 AN: 41404

American (AMR) AF: 0.146 AC: 2227 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3468

East Asian (EAS) AF: 0.0785 AC: 405 AN: 5160

South Asian (SAS) AF: 0.192 AC: 926 AN: 4820

European-Finnish (FIN) AF: 0.116 AC: 1221 AN: 10558

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8545 AN: 67992

Other (OTH) AF: 0.176 AC: 372 AN: 2108

Alfa AF: 0.120 Hom.: 661

Bravo AF: 0.166

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.35
PhyloP100		-0.28
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: rs3797980; hg19: chr5-9328316;