rs6867641

Variant names:

• chr5-33985752-T-C
• rs6867641

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 0.703 in 150,134 control chromosomes in the GnomAD database, including 37,680 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 0.70 (37680 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 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: 0.703 AC: 105428 AN: 150014 Hom.: 37651 Cov.: 29

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.703 AC: 105502 AN: 150134 Hom.: 37680 Cov.: 29 AF XY: 0.698 AC XY: 51164 AN XY: 73278

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.679

Alfa AF: 0.699 Hom.: 3450

Bravo AF: 0.715

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.70
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6867641; hg19: chr5-33985857;