6-43764117-C-T

Variant names:

• chr6-43764117-C-T
• rs833058

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 0.53 in 152,122 control chromosomes in the GnomAD database, including 23,949 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 (23949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 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: 0.529 AC: 80479 AN: 152004 Hom.: 23915 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.530 AC: 80579 AN: 152122 Hom.: 23949 Cov.: 32 AF XY: 0.531 AC XY: 39533 AN XY: 74382

African (AFR) AF: 0.802 AC: 33299 AN: 41498

American (AMR) AF: 0.541 AC: 8270 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3472

East Asian (EAS) AF: 0.725 AC: 3755 AN: 5178

South Asian (SAS) AF: 0.535 AC: 2584 AN: 4826

European-Finnish (FIN) AF: 0.386 AC: 4086 AN: 10580

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25617 AN: 67974

Other (OTH) AF: 0.530 AC: 1117 AN: 2108

Alfa AF: 0.459 Hom.: 8157

Bravo AF: 0.556

Asia WGS AF: 0.597 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.54
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs833058; hg19: chr6-43731854;