rs12634530

Variant names:

• chr3-124025623-C-T
• rs12634530
• ENST00000801819.1:n.81-6636C>T

Variant summary

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

The ENST00000801819.1(ENSG00000304291):​n.81-6636C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,982 control chromosomes in the GnomAD database, including 6,020 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 0.26 (6020 hom., cov: 32)
• Consequence: ENSG00000304291 ENST00000801819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 4 publications found

Genes affected

ENSG00000304291 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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
ENSG00000304291	ENST00000801819.1	n.81-6636C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40161 AN: 151864 Hom.: 6003 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.265 AC: 40213 AN: 151982 Hom.: 6020 Cov.: 32 AF XY: 0.268 AC XY: 19893 AN XY: 74282

African (AFR) AF: 0.388 AC: 16050 AN: 41386

American (AMR) AF: 0.265 AC: 4047 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2430 AN: 5170

South Asian (SAS) AF: 0.286 AC: 1373 AN: 4798

European-Finnish (FIN) AF: 0.236 AC: 2497 AN: 10560

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12366 AN: 67994

Other (OTH) AF: 0.283 AC: 599 AN: 2114

Alfa AF: 0.209 Hom.: 6240

Bravo AF: 0.275

Asia WGS AF: 0.396 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.68
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12634530; hg19: chr3-123744470;