rs4896243

Variant names:

• chr6-137193653-C-T
• rs4896243

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 0.612 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.914

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.636

Alfa AF: 0.547 Hom.: 22115

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4896243; hg19: chr6-137514790;