rs4897047

Variant names:

• chr6-125531475-T-C
• rs4897047

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 0.512 in 152,060 control chromosomes in the GnomAD database, including 22,766 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 0.51 (22766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 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: 0.513 AC: 77907 AN: 151942 Hom.: 22758 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.512 AC: 77928 AN: 152060 Hom.: 22766 Cov.: 32 AF XY: 0.520 AC XY: 38648 AN XY: 74312

African (AFR) AF: 0.216 AC: 8963 AN: 41504

American (AMR) AF: 0.633 AC: 9666 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1790 AN: 3466

East Asian (EAS) AF: 0.868 AC: 4488 AN: 5172

South Asian (SAS) AF: 0.594 AC: 2860 AN: 4816

European-Finnish (FIN) AF: 0.672 AC: 7102 AN: 10566

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41242 AN: 67956

Other (OTH) AF: 0.552 AC: 1167 AN: 2116

Alfa AF: 0.480 Hom.: 9959

Bravo AF: 0.501

Asia WGS AF: 0.698 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs4897047; hg19: chr6-125852621; COSMIC: COSV60279618;