chr6-43759219-T-C

Variant names:

• chr6-43759219-T-C
• rs866236

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 0.654 in 152,012 control chromosomes in the GnomAD database, including 33,918 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 0.65 (33918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 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: 0.654 AC: 99373 AN: 151894 Hom.: 33904 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.654 AC: 99405 AN: 152012 Hom.: 33918 Cov.: 32 AF XY: 0.649 AC XY: 48247 AN XY: 74298

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.665

Alfa AF: 0.745 Hom.: 73500

Bravo AF: 0.640

Asia WGS AF: 0.478 AC: 1661 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	0.014
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs866236; hg19: chr6-43726956;