6-122158600-G-A

Position:

• chr6-122158600-G-A

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 0.343 in 151,984 control chromosomes in the GnomAD database, including 9,456 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 0.34 (9456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52186 AN: 151864 Hom.: 9452 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.343 AC: 52204 AN: 151984 Hom.: 9456 Cov.: 32 AF XY: 0.354 AC XY: 26308 AN XY: 74258

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.348

Alfa AF: 0.322 Hom.: 996

Bravo AF: 0.348

Asia WGS AF: 0.418 AC: 1451 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	3.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1563512; hg19: chr6-122479746;