rs4896243

Variant names:

• chr6-137193653-C-T
• rs4896243

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 0.612 in 151,988 control chromosomes in the GnomAD database, including 29,771 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 0.61 (29771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 15 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 (EAS) allele frequency at 95% confidence interval = 0.893 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: 0.611 AC: 92838 AN: 151872 Hom.: 29715 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.612 AC: 92954 AN: 151988 Hom.: 29771 Cov.: 32 AF XY: 0.615 AC XY: 45674 AN XY: 74272

African (AFR) AF: 0.771 AC: 31956 AN: 41470

American (AMR) AF: 0.604 AC: 9218 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1930 AN: 3466

East Asian (EAS) AF: 0.914 AC: 4740 AN: 5184

South Asian (SAS) AF: 0.729 AC: 3511 AN: 4818

European-Finnish (FIN) AF: 0.461 AC: 4850 AN: 10516

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34829 AN: 67948

Other (OTH) AF: 0.636 AC: 1343 AN: 2110

Alfa AF: 0.558 Hom.: 37393

Bravo AF: 0.627

Asia WGS AF: 0.825 AC: 2866 AN: 3478

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	0.23
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4896243; hg19: chr6-137514790;