rs2044111

Variant names:

• chr5-22861294-G-A
• rs2044111

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.638 in 151,690 control chromosomes in the GnomAD database, including 31,507 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 0.64 (31507 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.693 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: 0.638 AC: 96754 AN: 151570 Hom.: 31494 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.638 AC: 96805 AN: 151690 Hom.: 31507 Cov.: 31 AF XY: 0.639 AC XY: 47389 AN XY: 74128

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.639

Alfa AF: 0.669 Hom.: 17041

Bravo AF: 0.634

Asia WGS AF: 0.527 AC: 1831 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2044111; hg19: chr5-22861403;