chr6-26072576-A-G

Variant names:

• chr6-26072576-A-G
• rs6942196

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 0.372 in 151,788 control chromosomes in the GnomAD database, including 11,344 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 0.37 (11344 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 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: 0.373 AC: 56518 AN: 151670 Hom.: 11342 Cov.: 30

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.372 AC: 56536 AN: 151788 Hom.: 11344 Cov.: 30 AF XY: 0.377 AC XY: 27990 AN XY: 74176

African (AFR) AF: 0.240 AC: 9930 AN: 41390

American (AMR) AF: 0.413 AC: 6310 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1091 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3629 AN: 5126

South Asian (SAS) AF: 0.376 AC: 1806 AN: 4798

European-Finnish (FIN) AF: 0.436 AC: 4582 AN: 10516

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.410 AC: 27877 AN: 67926

Other (OTH) AF: 0.382 AC: 802 AN: 2102

Alfa AF: 0.395 Hom.: 17127

Bravo AF: 0.367

Asia WGS AF: 0.520 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.3
DANN	Benign	0.86
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs6942196; hg19: chr6-26072804;