rs924043

Variant names:

• chr6-170063801-T-C
• rs924043

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 0.706 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.706 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

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.735

Alfa AF: 0.827 Hom.: 44649

Bravo AF: 0.680

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs924043; hg19: chr6-170379025;