6-43759293-G-T

Variant names:

• chr6-43759293-G-T
• rs833057

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 0.725 in 152,060 control chromosomes in the GnomAD database, including 40,481 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 0.72 (40481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.772 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: 0.725 AC: 110111 AN: 151942 Hom.: 40458 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.725 AC: 110170 AN: 152060 Hom.: 40481 Cov.: 32 AF XY: 0.718 AC XY: 53398 AN XY: 74326

African (AFR) AF: 0.696 AC: 28837 AN: 41444

American (AMR) AF: 0.663 AC: 10140 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2690 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2116 AN: 5160

South Asian (SAS) AF: 0.612 AC: 2948 AN: 4818

European-Finnish (FIN) AF: 0.779 AC: 8251 AN: 10590

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.777 AC: 52830 AN: 67976

Other (OTH) AF: 0.718 AC: 1515 AN: 2110

Alfa AF: 0.759 Hom.: 44850

Bravo AF: 0.720

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.84
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs833057; hg19: chr6-43727030;