rs924043

Variant names:

• chr6-170063801-T-C
• rs924043

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 0.706 in 151,880 control chromosomes in the GnomAD database, including 40,487 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 0.71 (40487 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107206 AN: 151762 Hom.: 40483 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.706 AC: 107235 AN: 151880 Hom.: 40487 Cov.: 31 AF XY: 0.704 AC XY: 52278 AN XY: 74252

African (AFR) AF: 0.446 AC: 18449 AN: 41346

American (AMR) AF: 0.707 AC: 10798 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2779 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2119 AN: 5126

South Asian (SAS) AF: 0.733 AC: 3528 AN: 4816

European-Finnish (FIN) AF: 0.824 AC: 8710 AN: 10576

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58218 AN: 67960

Other (OTH) AF: 0.735 AC: 1549 AN: 2108

Alfa AF: 0.800 Hom.: 144252

Bravo AF: 0.680

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.9
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs924043; hg19: chr6-170379025;