rs2789047

Variant names:

• chr6-120868656-C-A
• rs2789047

Your query was ambiguous. Multiple possible variants found:

• chr6-120868656-C-A
• chr6-120868656-C-G
• chr6-120868656-C-T

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 0.44 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.684 AC: 28319 AN: 41400

American (AMR) AF: 0.561 AC: 8550 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1325 AN: 3466

East Asian (EAS) AF: 0.596 AC: 3069 AN: 5152

South Asian (SAS) AF: 0.527 AC: 2529 AN: 4796

European-Finnish (FIN) AF: 0.204 AC: 2141 AN: 10520

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19534 AN: 67828

Other (OTH) AF: 0.438 AC: 920 AN: 2102

Alfa AF: 0.355 Hom.: 8019

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2789047; hg19: chr6-121189802;