chr6-43762907-A-T

Variant names:

• chr6-43762907-A-T
• rs1547651

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 0.15 in 152,194 control chromosomes in the GnomAD database, including 1,685 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 0.15 (1685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22758 AN: 152074 Hom.: 1685 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.150 AC: 22772 AN: 152194 Hom.: 1685 Cov.: 32 AF XY: 0.152 AC XY: 11305 AN XY: 74428

African (AFR) AF: 0.126 AC: 5227 AN: 41520

American (AMR) AF: 0.141 AC: 2162 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3472

East Asian (EAS) AF: 0.103 AC: 535 AN: 5172

South Asian (SAS) AF: 0.148 AC: 715 AN: 4826

European-Finnish (FIN) AF: 0.178 AC: 1891 AN: 10596

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11255 AN: 67990

Other (OTH) AF: 0.129 AC: 273 AN: 2114

Alfa AF: 0.0929 Hom.: 121

Bravo AF: 0.140

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.42
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1547651; hg19: chr6-43730644;