rs1082714

Variant names:

• chr12-67235051-C-T
• rs1082714

Variant summary

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

The variant allele was found at a frequency of 0.427 in 151,926 control chromosomes in the GnomAD database, including 16,492 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 0.43 (16492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 12 publications found

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 = 0.703 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

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64804 AN: 151808 Hom.: 16457 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.427 AC: 64885 AN: 151926 Hom.: 16492 Cov.: 32 AF XY: 0.427 AC XY: 31681 AN XY: 74228

African (AFR) AF: 0.710 AC: 29431 AN: 41456

American (AMR) AF: 0.309 AC: 4712 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3464

East Asian (EAS) AF: 0.582 AC: 3002 AN: 5158

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4820

European-Finnish (FIN) AF: 0.366 AC: 3853 AN: 10538

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19923 AN: 67926

Other (OTH) AF: 0.378 AC: 797 AN: 2108

Alfa AF: 0.343 Hom.: 10597

Bravo AF: 0.439

Asia WGS AF: 0.420 AC: 1461 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs1082714; hg19: chr12-67628831;