ENST00000811253.1:n.149-37499G>A

Variant names:

• chr2-57706920-C-T
• rs13026414
• ENST00000811253.1:n.149-37499G>A

Variant summary

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

The ENST00000811253.1(ENSG00000285755):​n.149-37499G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,104 control chromosomes in the GnomAD database, including 7,766 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 (7766 hom., cov: 32)
• Consequence: ENSG00000285755 ENST00000811253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 22 publications found

Genes affected

ENSG00000285755 (HGNC:58935):

ENSG00000305509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 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.149-37499G>A		intron	N/A
	ENSG00000285755	ENST00000811255.1		n.396+14029G>A		intron	N/A
	ENSG00000305509	ENST00000811399.1		n.392+10778C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44146 AN: 151986 Hom.: 7769 Cov.: 32

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.290 AC: 44136 AN: 152104 Hom.: 7766 Cov.: 32 AF XY: 0.282 AC XY: 20962 AN XY: 74360

African (AFR) AF: 0.0967 AC: 4017 AN: 41538

American (AMR) AF: 0.329 AC: 5029 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3466

East Asian (EAS) AF: 0.204 AC: 1057 AN: 5176

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4824

European-Finnish (FIN) AF: 0.278 AC: 2939 AN: 10566

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27301 AN: 67942

Other (OTH) AF: 0.337 AC: 709 AN: 2104

Alfa AF: 0.351 Hom.: 20552

Bravo AF: 0.289

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.99
DANN	Benign	0.56
PhyloP100		-0.70

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: rs13026414;

hg19: chr2-57934055;