rs6801844

Variant names:

• chr3-42237593-G-A
• rs6801844

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 0.353 in 151,868 control chromosomes in the GnomAD database, including 11,111 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 0.35 (11111 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.352 AC: 53486 AN: 151750 Hom.: 11087 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.353 AC: 53561 AN: 151868 Hom.: 11111 Cov.: 32 AF XY: 0.357 AC XY: 26495 AN XY: 74232

African (AFR) AF: 0.531 AC: 21984 AN: 41398

American (AMR) AF: 0.373 AC: 5690 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 688 AN: 3466

East Asian (EAS) AF: 0.736 AC: 3800 AN: 5162

South Asian (SAS) AF: 0.277 AC: 1330 AN: 4804

European-Finnish (FIN) AF: 0.311 AC: 3275 AN: 10538

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15868 AN: 67936

Other (OTH) AF: 0.324 AC: 682 AN: 2108

Alfa AF: 0.275 Hom.: 4900

Bravo AF: 0.370

Asia WGS AF: 0.487 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.38
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs6801844; hg19: chr3-42279085;