rs2515192

Variant names:

• chr8-103019945-A-G
• rs2515192
• ENST00000522416.1:n.*242T>C

Variant summary

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

The ENST00000522416.1(ENSG00000254236):​n.*242T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,098 control chromosomes in the GnomAD database, including 28,159 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 0.58 (28159 hom., cov: 32)
• Consequence: ENSG00000254236 ENST00000522416.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 4 publications found

Genes affected

ENSG00000254236 (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 (AFR) allele frequency at 95% confidence interval = 0.855 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
ENSG00000254236	ENST00000522416.1	n.*242T>C		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88251 AN: 151980 Hom.: 28092 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.581 AC: 88373 AN: 152098 Hom.: 28159 Cov.: 32 AF XY: 0.574 AC XY: 42647 AN XY: 74330

African (AFR) AF: 0.862 AC: 35797 AN: 41512

American (AMR) AF: 0.452 AC: 6903 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2076 AN: 5184

South Asian (SAS) AF: 0.436 AC: 2103 AN: 4822

European-Finnish (FIN) AF: 0.445 AC: 4703 AN: 10558

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33467 AN: 67958

Other (OTH) AF: 0.522 AC: 1102 AN: 2110

Alfa AF: 0.534 Hom.: 13845

Bravo AF: 0.595

Asia WGS AF: 0.423 AC: 1475 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	3.4
DANN	Benign	0.68
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2515192; hg19: chr8-104032173;