2-57714152-A-G

Variant names:

• chr2-57714152-A-G
• rs1380703
• ENST00000811253.1:n.149-44731T>C

Variant summary

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

The ENST00000811253.1(ENSG00000285755):​n.149-44731T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,116 control chromosomes in the GnomAD database, including 8,677 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 0.31 (8677 hom., cov: 32)
• Consequence: ENSG00000285755 ENST00000811253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 16 publications found

Genes affected

ENSG00000285755 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 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
ENSG00000285755	ENST00000811253.1	n.149-44731T>C		intron_variant	Intron 2 of 2
ENSG00000285755	ENST00000811255.1	n.396+6797T>C		intron_variant	Intron 1 of 2
ENSG00000305509	ENST00000811399.1	n.393-11543A>G		intron_variant	Intron 2 of 2
ENSG00000305509	ENST00000811400.1	n.134-11543A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47800 AN: 151998 Hom.: 8674 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.314 AC: 47818 AN: 152116 Hom.: 8677 Cov.: 32 AF XY: 0.320 AC XY: 23781 AN XY: 74346

African (AFR) AF: 0.134 AC: 5574 AN: 41524

American (AMR) AF: 0.331 AC: 5053 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2806 AN: 5180

South Asian (SAS) AF: 0.497 AC: 2398 AN: 4824

European-Finnish (FIN) AF: 0.356 AC: 3753 AN: 10552

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25791 AN: 67968

Other (OTH) AF: 0.360 AC: 762 AN: 2114

Alfa AF: 0.355 Hom.: 18315

Bravo AF: 0.303

Asia WGS AF: 0.516 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.82
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1380703; hg19: chr2-57941287;