rs6444087

Variant names:

• chr3-185904041-G-A
• rs6444087

Your query was ambiguous. Multiple possible variants found:

• chr3-185904041-G-A
• chr3-185904041-G-C

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 0.726 in 151,402 control chromosomes in the GnomAD database, including 40,005 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 (40005 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.768 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: 0.726 AC: 109774 AN: 151296 Hom.: 39984 Cov.: 29

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.726 AC: 109851 AN: 151402 Hom.: 40005 Cov.: 29 AF XY: 0.723 AC XY: 53487 AN XY: 73936

African (AFR) AF: 0.716 AC: 29562 AN: 41262

American (AMR) AF: 0.694 AC: 10532 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2425 AN: 3466

East Asian (EAS) AF: 0.691 AC: 3567 AN: 5160

South Asian (SAS) AF: 0.789 AC: 3794 AN: 4808

European-Finnish (FIN) AF: 0.706 AC: 7305 AN: 10340

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.740 AC: 50252 AN: 67882

Other (OTH) AF: 0.715 AC: 1504 AN: 2104

Alfa AF: 0.733 Hom.: 181761

Bravo AF: 0.723

Asia WGS AF: 0.736 AC: 2561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.44
DANN	Benign	0.88
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs6444087; hg19: chr3-185621829;