rs789942

Variant names:

• chr6-63093283-C-A
• rs789942

Your query was ambiguous. Multiple possible variants found:

• chr6-63093283-C-A
• chr6-63093283-C-G
• chr6-63093283-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 0.728 in 152,054 control chromosomes in the GnomAD database, including 40,613 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 0.73 (40613 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 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: 0.728 AC: 110648 AN: 151936 Hom.: 40598 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.728 AC: 110705 AN: 152054 Hom.: 40613 Cov.: 32 AF XY: 0.728 AC XY: 54076 AN XY: 74320

African (AFR) AF: 0.768 AC: 31867 AN: 41486

American (AMR) AF: 0.665 AC: 10144 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3458 AN: 5160

South Asian (SAS) AF: 0.577 AC: 2776 AN: 4810

European-Finnish (FIN) AF: 0.834 AC: 8819 AN: 10580

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48777 AN: 67974

Other (OTH) AF: 0.716 AC: 1513 AN: 2112

Alfa AF: 0.716 Hom.: 94878

Bravo AF: 0.720

Asia WGS AF: 0.584 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs789942; hg19: chr6-63803188;