rs12492095

Positions:

• chr3-124729109-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000683807.1(ENSG00000288713):​n.78+1236A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,222 control chromosomes in the GnomAD database, including 2,464 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 (2464 hom., cov: 31)
• Consequence: ENST00000683807.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000683807.1	n.78+1236A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26178 AN: 152104 Hom.: 2461 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.0993

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.172 AC: 26191 AN: 152222 Hom.: 2464 Cov.: 31 AF XY: 0.175 AC XY: 13009 AN XY: 74426

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.0993

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.171

Alfa AF: 0.165 Hom.: 278

Bravo AF: 0.174

Asia WGS AF: 0.188 AC: 654 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	3.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12492095; hg19: chr3-124447956;