chr2-151354289-A-T

Variant names:

• chr2-151354289-A-T
• rs2342910
• ENST00000731384.1:n.177-14890T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000731384.1(ENSG00000295625):​n.177-14890T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,146 control chromosomes in the GnomAD database, including 5,412 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 0.25 (5412 hom., cov: 32)
• Consequence: ENSG00000295625 ENST00000731384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 6 publications found

Genes affected

ENSG00000295625 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929319	NR_110248.1	n.307-14890T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295625	ENST00000731384.1	n.177-14890T>A		intron_variant	Intron 2 of 2
ENSG00000295625	ENST00000731385.1	n.176-14887T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38029 AN: 152028 Hom.: 5399 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.250 AC: 38063 AN: 152146 Hom.: 5412 Cov.: 32 AF XY: 0.248 AC XY: 18432 AN XY: 74380

African (AFR) AF: 0.140 AC: 5829 AN: 41514

American (AMR) AF: 0.193 AC: 2949 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1140 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2032 AN: 5178

South Asian (SAS) AF: 0.372 AC: 1795 AN: 4828

European-Finnish (FIN) AF: 0.228 AC: 2413 AN: 10562

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20756 AN: 67988

Other (OTH) AF: 0.288 AC: 607 AN: 2110

Alfa AF: 0.272 Hom.: 715

Bravo AF: 0.239

Asia WGS AF: 0.376 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs2342910; hg19: chr2-152210803;