6-120868656-C-A

Position:

• chr6-120868656-C-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 0.44 in 151,694 control chromosomes in the GnomAD database, including 17,361 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 0.44 (17361 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

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 (AFR) allele frequency at 95% confidence interval = 0.677 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: 0.439 AC: 66568 AN: 151574 Hom.: 17312 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.440 AC: 66682 AN: 151694 Hom.: 17361 Cov.: 31 AF XY: 0.441 AC XY: 32671 AN XY: 74142

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.438

Alfa AF: 0.309 Hom.: 3962

Bravo AF: 0.476

Asia WGS AF: 0.584 AC: 2032 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	1.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2789047; hg19: chr6-121189802;