rs6924357

Variant names:

• chr6-166180964-T-A
• rs6924357

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 0.535 in 152,136 control chromosomes in the GnomAD database, including 22,411 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 0.53 (22411 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 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: 0.535 AC: 81266 AN: 152018 Hom.: 22391 Cov.: 33

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.535 AC: 81326 AN: 152136 Hom.: 22411 Cov.: 33 AF XY: 0.524 AC XY: 38984 AN XY: 74392

African (AFR) AF: 0.538 AC: 22341 AN: 41504

American (AMR) AF: 0.468 AC: 7137 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2031 AN: 3472

East Asian (EAS) AF: 0.107 AC: 556 AN: 5186

South Asian (SAS) AF: 0.516 AC: 2491 AN: 4826

European-Finnish (FIN) AF: 0.469 AC: 4968 AN: 10588

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.588 AC: 39967 AN: 67988

Other (OTH) AF: 0.530 AC: 1116 AN: 2104

Alfa AF: 0.561 Hom.: 2976

Bravo AF: 0.533

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.55
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs6924357; hg19: chr6-166594452; COSMIC: COSV60302332;