6-126273121-G-A

Variant names:

• chr6-126273121-G-A
• rs643394

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 0.223 in 152,084 control chromosomes in the GnomAD database, including 4,945 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 0.22 (4945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 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: 0.223 AC: 33898 AN: 151966 Hom.: 4927 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.0902

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.223 AC: 33961 AN: 152084 Hom.: 4945 Cov.: 32 AF XY: 0.225 AC XY: 16754 AN XY: 74360

African (AFR) AF: 0.359 AC: 14894 AN: 41474

American (AMR) AF: 0.284 AC: 4341 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3468

East Asian (EAS) AF: 0.511 AC: 2645 AN: 5174

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4816

European-Finnish (FIN) AF: 0.0902 AC: 955 AN: 10586

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8331 AN: 67980

Other (OTH) AF: 0.228 AC: 480 AN: 2108

Alfa AF: 0.162 Hom.: 11276

Bravo AF: 0.243

Asia WGS AF: 0.372 AC: 1293 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	0.14
DANN	Benign	0.13
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs643394; hg19: chr6-126594267;