rs924043

chr6-170063801-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;