rs2619097

Variant names:

• chr10-117233073-C-A
• rs2619097
• ENST00000756185.1:n.166+486C>A

Variant summary

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

The ENST00000756185.1(ENSG00000298523):​n.166+486C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,000 control chromosomes in the GnomAD database, including 49,811 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 0.78 (49811 hom., cov: 31)
• Consequence: ENSG00000298523 ENST00000756185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 2 publications found

Genes affected

ENSG00000298523 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.928 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
ENSG00000298523	ENST00000756185.1	n.166+486C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118920 AN: 151882 Hom.: 49802 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.783 AC: 118961 AN: 152000 Hom.: 49811 Cov.: 31 AF XY: 0.786 AC XY: 58432 AN XY: 74352

African (AFR) AF: 0.460 AC: 19035 AN: 41338

American (AMR) AF: 0.779 AC: 11905 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3169 AN: 3470

East Asian (EAS) AF: 0.779 AC: 4011 AN: 5148

South Asian (SAS) AF: 0.902 AC: 4354 AN: 4828

European-Finnish (FIN) AF: 0.954 AC: 10128 AN: 10618

Middle Eastern (MID) AF: 0.860 AC: 251 AN: 292

European-Non Finnish (NFE) AF: 0.934 AC: 63530 AN: 68008

Other (OTH) AF: 0.801 AC: 1690 AN: 2110

Alfa AF: 0.841 Hom.: 7025

Bravo AF: 0.749

Asia WGS AF: 0.811 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.83
DANN	Benign	0.60
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2619097; hg19: chr10-118992584;