5-9452977-C-A

Variant names:

• chr5-9452977-C-A
• rs436243
• NM_003966.3:c.-174-15125G>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.-174-15125G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,242 control chromosomes in the GnomAD database, including 63,722 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 0.91 (63722 hom., cov: 32)
• Consequence: SEMA5A NM_003966.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA5A	NM_003966.3	c.-174-15125G>T		intron_variant	Intron 1 of 22	ENST00000382496.10	NP_003957.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEMA5A	ENST00000382496.10	c.-174-15125G>T		intron_variant	Intron 1 of 22	1	NM_003966.3	ENSP00000371936.5
SEMA5A	ENST00000652226.1	c.-392-15125G>T		intron_variant	Intron 1 of 24			ENSP00000499013.1

Frequencies

GnomAD3 genomes AF: 0.914 AC: 139018 AN: 152124 Hom.: 63673 Cov.: 32

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.914 AC: 139127 AN: 152242 Hom.: 63722 Cov.: 32 AF XY: 0.911 AC XY: 67802 AN XY: 74426

African (AFR) AF: 0.964 AC: 40064 AN: 41554

American (AMR) AF: 0.900 AC: 13778 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3019 AN: 3468

East Asian (EAS) AF: 0.764 AC: 3942 AN: 5158

South Asian (SAS) AF: 0.853 AC: 4113 AN: 4822

European-Finnish (FIN) AF: 0.904 AC: 9580 AN: 10596

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61716 AN: 68028

Other (OTH) AF: 0.902 AC: 1901 AN: 2108

Alfa AF: 0.905 Hom.: 93668

Bravo AF: 0.916

Asia WGS AF: 0.825 AC: 2870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.62
DANN	Benign	0.35
PhyloP100		-1.4
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: rs436243; hg19: chr5-9453089;