6-132409233-C-G

Variant names:

• chr6-132409233-C-G
• rs7743622

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 0.695 in 152,024 control chromosomes in the GnomAD database, including 38,204 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 0.70 (38204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.928 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: 0.695 AC: 105560 AN: 151906 Hom.: 38140 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.695 AC: 105682 AN: 152024 Hom.: 38204 Cov.: 32 AF XY: 0.699 AC XY: 51967 AN XY: 74318

African (AFR) AF: 0.867 AC: 35993 AN: 41520

American (AMR) AF: 0.749 AC: 11437 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2179 AN: 3468

East Asian (EAS) AF: 0.951 AC: 4920 AN: 5176

South Asian (SAS) AF: 0.706 AC: 3392 AN: 4804

European-Finnish (FIN) AF: 0.602 AC: 6356 AN: 10554

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.578 AC: 39265 AN: 67912

Other (OTH) AF: 0.701 AC: 1481 AN: 2112

Alfa AF: 0.645 Hom.: 3834

Bravo AF: 0.712

Asia WGS AF: 0.838 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7743622; hg19: chr6-132730372;