rs1547251

Variant names:

• chr6-82696390-C-T
• rs1547251

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.472

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

Splicing

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

Publications

LitVar

Other links and lift over

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