rs2044844

Variant names:

• chr4-42854622-C-A
• rs2044844

Your query was ambiguous. Multiple possible variants found:

• chr4-42854622-C-A
• chr4-42854622-C-G

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 0.755 in 151,908 control chromosomes in the GnomAD database, including 45,063 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 0.76 (45063 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 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: 0.755 AC: 114647 AN: 151790 Hom.: 45049 Cov.: 30

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.755 AC: 114708 AN: 151908 Hom.: 45063 Cov.: 30 AF XY: 0.752 AC XY: 55863 AN XY: 74258

African (AFR) AF: 0.545 AC: 22526 AN: 41346

American (AMR) AF: 0.790 AC: 12049 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3136 AN: 3472

East Asian (EAS) AF: 0.550 AC: 2833 AN: 5148

South Asian (SAS) AF: 0.643 AC: 3099 AN: 4818

European-Finnish (FIN) AF: 0.875 AC: 9259 AN: 10586

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59221 AN: 67976

Other (OTH) AF: 0.790 AC: 1668 AN: 2112

Alfa AF: 0.829 Hom.: 27110

Bravo AF: 0.741

Asia WGS AF: 0.618 AC: 2154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.39
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2044844; hg19: chr4-42856639;