rs2044111

Variant names:

• chr5-22861294-G-A
• rs2044111
• ENST00000799148.1:n.265+288G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000799148.1(ENSG00000304054):​n.265+288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000304054 ENST00000799148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 3 publications found

Genes affected

ENSG00000304054 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000304054	ENST00000799148.1	n.265+288G>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.533 AC: 22066 AN: 41370

American (AMR) AF: 0.705 AC: 10734 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2413 AN: 3462

East Asian (EAS) AF: 0.466 AC: 2396 AN: 5146

South Asian (SAS) AF: 0.566 AC: 2724 AN: 4814

European-Finnish (FIN) AF: 0.714 AC: 7535 AN: 10554

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46794 AN: 67798

Other (OTH) AF: 0.639 AC: 1347 AN: 2108

Alfa AF: 0.663 Hom.: 24205

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2044111; hg19: chr5-22861403;