rs1547251

Variant names:

• chr6-82696390-C-T
• rs1547251

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 0.433 in 151,908 control chromosomes in the GnomAD database, including 17,200 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 (17200 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 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: 0.433 AC: 65708 AN: 151792 Hom.: 17203 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.433 AC: 65719 AN: 151908 Hom.: 17200 Cov.: 31 AF XY: 0.438 AC XY: 32530 AN XY: 74200

African (AFR) AF: 0.126 AC: 5243 AN: 41454

American (AMR) AF: 0.583 AC: 8900 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2177 AN: 3468

East Asian (EAS) AF: 0.764 AC: 3937 AN: 5154

South Asian (SAS) AF: 0.577 AC: 2773 AN: 4810

European-Finnish (FIN) AF: 0.496 AC: 5208 AN: 10510

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35851 AN: 67938

Other (OTH) AF: 0.472 AC: 996 AN: 2108

Alfa AF: 0.485 Hom.: 3299

Bravo AF: 0.427

Asia WGS AF: 0.630 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.78
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1547251; hg19: chr6-83406107; COSMIC: COSV69409663;