rs12637095

Variant names:

• chr3-118473456-T-A
• rs12637095
• ENST00000482142.5:n.232+23167A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-118473456-T-A
• chr3-118473456-T-C
• chr3-118473456-T-G

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+23167A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 151,914 control chromosomes in the GnomAD database, including 39,480 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 (39480 hom., cov: 31)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 3 publications found

Genes affected

ENSG00000243276 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243276	ENST00000482142.5	n.232+23167A>T		intron_variant	Intron 3 of 6	5
ENSG00000243276	ENST00000833975.1	n.448+23167A>T		intron_variant	Intron 5 of 5
ENSG00000243276	ENST00000833976.1	n.349+23167A>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107932 AN: 151796 Hom.: 39466 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.711 AC: 107994 AN: 151914 Hom.: 39480 Cov.: 31 AF XY: 0.716 AC XY: 53168 AN XY: 74236

African (AFR) AF: 0.511 AC: 21163 AN: 41378

American (AMR) AF: 0.741 AC: 11312 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2637 AN: 3466

East Asian (EAS) AF: 0.922 AC: 4761 AN: 5164

South Asian (SAS) AF: 0.820 AC: 3942 AN: 4808

European-Finnish (FIN) AF: 0.760 AC: 8019 AN: 10554

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53529 AN: 67964

Other (OTH) AF: 0.755 AC: 1590 AN: 2106

Alfa AF: 0.743 Hom.: 5299

Bravo AF: 0.701

Asia WGS AF: 0.828 AC: 2880 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	0.34
DANN	Benign	0.76
PhyloP100		-0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12637095; hg19: chr3-118192303;