6-43790159-C-A

Variant names:

• chr6-43790159-C-A
• rs998584

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 0.417 in 151,950 control chromosomes in the GnomAD database, including 14,752 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 0.42 (14752 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 149 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 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: 0.417 AC: 63275 AN: 151832 Hom.: 14742 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.417 AC: 63311 AN: 151950 Hom.: 14752 Cov.: 31 AF XY: 0.426 AC XY: 31602 AN XY: 74248

African (AFR) AF: 0.197 AC: 8180 AN: 41440

American (AMR) AF: 0.499 AC: 7618 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1844 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2838 AN: 5164

South Asian (SAS) AF: 0.674 AC: 3238 AN: 4806

European-Finnish (FIN) AF: 0.504 AC: 5305 AN: 10522

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32663 AN: 67972

Other (OTH) AF: 0.421 AC: 889 AN: 2110

Alfa AF: 0.461 Hom.: 51144

Bravo AF: 0.403

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs998584; hg19: chr6-43757896;