rs56015515

Variant names:

• chr2-85498231-G-A
• rs56015515
• ENST00000793246.1:n.141+18505C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-85498231-G-A
• chr2-85498231-G-C
• chr2-85498231-G-T

Variant summary

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

The ENST00000793246.1(ENSG00000303258):​n.141+18505C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,006 control chromosomes in the GnomAD database, including 2,580 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 0.18 (2580 hom., cov: 32)
• Consequence: ENSG00000303258 ENST00000793246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 3 publications found

Genes affected

ENSG00000303258 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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
ENSG00000303258	ENST00000793246.1	n.141+18505C>T		intron_variant	Intron 1 of 1
ENSG00000303258	ENST00000793247.1	n.346+1802C>T		intron_variant	Intron 1 of 1
ENSG00000303258	ENST00000793248.1	n.339+1802C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26649 AN: 151888 Hom.: 2579 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.175 AC: 26661 AN: 152006 Hom.: 2580 Cov.: 32 AF XY: 0.174 AC XY: 12943 AN XY: 74300

African (AFR) AF: 0.134 AC: 5548 AN: 41464

American (AMR) AF: 0.156 AC: 2374 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3470

East Asian (EAS) AF: 0.0397 AC: 206 AN: 5186

South Asian (SAS) AF: 0.0693 AC: 333 AN: 4808

European-Finnish (FIN) AF: 0.264 AC: 2784 AN: 10534

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14141 AN: 67968

Other (OTH) AF: 0.182 AC: 385 AN: 2114

Alfa AF: 0.180 Hom.: 1344

Bravo AF: 0.166

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.31
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs56015515; hg19: chr2-85725354;