chr6-43769749-C-T

Variant names:

• chr6-43769749-C-T
• rs833061

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 0.559 in 151,884 control chromosomes in the GnomAD database, including 24,103 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 0.56 (24103 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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: 0.559 AC: 84807 AN: 151766 Hom.: 24081 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.559 AC: 84887 AN: 151884 Hom.: 24103 Cov.: 31 AF XY: 0.557 AC XY: 41324 AN XY: 74228

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.583

Alfa AF: 0.520 Hom.: 6149

Bravo AF: 0.578

Asia WGS AF: 0.606 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs833061; hg19: chr6-43737486;