6-120868656-C-A

Variant names:

• chr6-120868656-C-A
• rs2789047

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;