2-57744208-A-G

Variant names:

• chr2-57744208-A-G
• rs2125925
• ENST00000811253.1:n.148+38085T>C

Variant summary

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

The ENST00000811253.1(ENSG00000285755):​n.148+38085T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,880 control chromosomes in the GnomAD database, including 35,802 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 0.68 (35802 hom., cov: 31)
• Consequence: ENSG00000285755 ENST00000811253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 3 publications found

Genes affected

ENSG00000285755 (HGNC:58935):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811253.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285755	ENST00000811253.1		n.148+38085T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103390 AN: 151760 Hom.: 35757 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.681 AC: 103496 AN: 151880 Hom.: 35802 Cov.: 31 AF XY: 0.677 AC XY: 50220 AN XY: 74226

African (AFR) AF: 0.818 AC: 33944 AN: 41478

American (AMR) AF: 0.610 AC: 9288 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2294 AN: 3466

East Asian (EAS) AF: 0.619 AC: 3187 AN: 5150

South Asian (SAS) AF: 0.575 AC: 2768 AN: 4816

European-Finnish (FIN) AF: 0.649 AC: 6861 AN: 10566

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42894 AN: 67880

Other (OTH) AF: 0.659 AC: 1388 AN: 2106

Alfa AF: 0.585 Hom.: 3747

Bravo AF: 0.685

Asia WGS AF: 0.613 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.1
DANN	Benign	0.79
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs2125925; hg19: chr2-57971343;