rs1237758

Variant names:

• chr2-81761258-G-A
• rs1237758
• ENST00000798760.1:n.237+15870C>T

Variant summary

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

The ENST00000798760.1(ENSG00000303999):​n.237+15870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,842 control chromosomes in the GnomAD database, including 10,506 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 0.36 (10506 hom., cov: 31)
• Consequence: ENSG00000303999 ENST00000798760.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 4 publications found

Genes affected

ENSG00000303999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724542	NR_187691.1	n.498-87495G>A		intron_variant	Intron 2 of 3
LOC102724542	NR_187692.1	n.576-87495G>A		intron_variant	Intron 3 of 4
LOC102724542	NR_187693.1	n.498-36560G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303999	ENST00000798760.1	n.237+15870C>T		intron_variant	Intron 3 of 6
ENSG00000303999	ENST00000798761.1	n.428-120C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54711 AN: 151724 Hom.: 10504 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.360 AC: 54728 AN: 151842 Hom.: 10506 Cov.: 31 AF XY: 0.362 AC XY: 26830 AN XY: 74202

African (AFR) AF: 0.274 AC: 11367 AN: 41418

American (AMR) AF: 0.275 AC: 4182 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1334 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1119 AN: 5140

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4816

European-Finnish (FIN) AF: 0.512 AC: 5398 AN: 10544

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28683 AN: 67912

Other (OTH) AF: 0.332 AC: 703 AN: 2116

Alfa AF: 0.395 Hom.: 46463

Bravo AF: 0.338

Asia WGS AF: 0.254 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.75
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1237758; hg19: chr2-81988382;