6-122297552-A-G

Position:

• chr6-122297552-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.645

Alfa AF: 0.519 Hom.: 1501

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225083; hg19: chr6-122618698;