chr2-57462898-A-G

Variant names:

• chr2-57462898-A-G
• rs7589636
• ENST00000811252.1:n.147-82768T>C

Variant summary

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

The ENST00000811252.1(ENSG00000285755):​n.147-82768T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,080 control chromosomes in the GnomAD database, including 6,733 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 0.29 (6733 hom., cov: 32)
• Consequence: ENSG00000285755 ENST00000811252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.930
• Publications: 5 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811252.1. 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	ENST00000811252.1		n.147-82768T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43592 AN: 151962 Hom.: 6726 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.287 AC: 43628 AN: 152080 Hom.: 6733 Cov.: 32 AF XY: 0.295 AC XY: 21928 AN XY: 74338

African (AFR) AF: 0.371 AC: 15411 AN: 41492

American (AMR) AF: 0.303 AC: 4634 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2669 AN: 5162

South Asian (SAS) AF: 0.260 AC: 1256 AN: 4826

European-Finnish (FIN) AF: 0.317 AC: 3354 AN: 10580

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14608 AN: 67960

Other (OTH) AF: 0.276 AC: 582 AN: 2110

Alfa AF: 0.231 Hom.: 11936

Bravo AF: 0.295

Asia WGS AF: 0.305 AC: 1056 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		0.93

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7589636;

hg19: chr2-57690033;