rs2044111

chr5-22861294-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;