rs817015

Variant names:

• chr2-49373284-A-G
• rs817015
• ENST00000634539.1:n.103-33710T>C

Variant summary

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

The ENST00000634539.1(ENSG00000282998):​n.103-33710T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0981 in 152,240 control chromosomes in the GnomAD database, including 770 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 0.098 (770 hom., cov: 32)
• Consequence: ENSG00000282998 ENST00000634539.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 1 publications found

Genes affected

ENSG00000282998 (HGNC:):

ENSG00000282890 (HGNC:58158):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 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
ENSG00000282998	ENST00000634539.1	n.103-33710T>C		intron_variant	Intron 1 of 3	5
ENSG00000282890	ENST00000634588.1	n.493-34918A>G		intron_variant	Intron 2 of 4	5
ENSG00000282998	ENST00000635306.2	n.301-41304T>C		intron_variant	Intron 2 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 14913 AN: 152122 Hom.: 765 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.0981 AC: 14937 AN: 152240 Hom.: 770 Cov.: 32 AF XY: 0.0937 AC XY: 6977 AN XY: 74456

African (AFR) AF: 0.121 AC: 5026 AN: 41534

American (AMR) AF: 0.0595 AC: 911 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3466

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4824

European-Finnish (FIN) AF: 0.0771 AC: 819 AN: 10620

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7301 AN: 67986

Other (OTH) AF: 0.0964 AC: 204 AN: 2116

Alfa AF: 0.110 Hom.: 111

Bravo AF: 0.0966

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.48
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs817015; hg19: chr2-49600423;