6-122297552-A-G

Variant names:

• chr6-122297552-A-G
• rs225083

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 0.641 in 151,780 control chromosomes in the GnomAD database, including 31,351 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 0.64 (31351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) 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: 0.641 AC: 97254 AN: 151662 Hom.: 31333 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.641 AC: 97323 AN: 151780 Hom.: 31351 Cov.: 32 AF XY: 0.646 AC XY: 47902 AN XY: 74162

African (AFR) AF: 0.649 AC: 26862 AN: 41390

American (AMR) AF: 0.728 AC: 11082 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2229 AN: 3466

East Asian (EAS) AF: 0.670 AC: 3444 AN: 5140

South Asian (SAS) AF: 0.793 AC: 3820 AN: 4818

European-Finnish (FIN) AF: 0.606 AC: 6402 AN: 10568

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41430 AN: 67874

Other (OTH) AF: 0.645 AC: 1359 AN: 2106

Alfa AF: 0.530 Hom.: 1682

Bravo AF: 0.649

Asia WGS AF: 0.723 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.28
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs225083; hg19: chr6-122618698;