3-44241442-G-A

Variant names:

• chr3-44241442-G-A
• rs9809107

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 0.473 in 152,108 control chromosomes in the GnomAD database, including 17,906 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 0.47 (17906 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 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: 0.473 AC: 71929 AN: 151990 Hom.: 17890 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.473 AC: 71987 AN: 152108 Hom.: 17906 Cov.: 33 AF XY: 0.481 AC XY: 35796 AN XY: 74370

African (AFR) AF: 0.366 AC: 15170 AN: 41494

American (AMR) AF: 0.543 AC: 8307 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1833 AN: 3470

East Asian (EAS) AF: 0.805 AC: 4149 AN: 5156

South Asian (SAS) AF: 0.703 AC: 3393 AN: 4824

European-Finnish (FIN) AF: 0.508 AC: 5377 AN: 10588

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32171 AN: 67962

Other (OTH) AF: 0.467 AC: 986 AN: 2112

Alfa AF: 0.478 Hom.: 43980

Bravo AF: 0.471

Asia WGS AF: 0.724 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.8
DANN	Benign	0.83
PhyloP100		-0.18
PromoterAI		0.012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9809107; hg19: chr3-44282934;