rs17158139

Variant names:

• chr10-2319919-T-A
• rs17158139
• ENST00000721486.1:n.669+391T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-2319919-T-A
• chr10-2319919-T-C

Variant summary

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

The ENST00000721486.1(ENSG00000294151):​n.669+391T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,100 control chromosomes in the GnomAD database, including 1,781 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 0.12 (1781 hom., cov: 33)
• Consequence: ENSG00000294151 ENST00000721486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 2 publications found

Genes affected

ENSG00000294151 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376349	XR_930551.2	n.188+1305T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294151	ENST00000721486.1	n.669+391T>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17630 AN: 151982 Hom.: 1773 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0368

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.116 AC: 17672 AN: 152100 Hom.: 1781 Cov.: 33 AF XY: 0.118 AC XY: 8777 AN XY: 74384

African (AFR) AF: 0.267 AC: 11073 AN: 41426

American (AMR) AF: 0.0917 AC: 1401 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3470

East Asian (EAS) AF: 0.130 AC: 670 AN: 5170

South Asian (SAS) AF: 0.160 AC: 770 AN: 4812

European-Finnish (FIN) AF: 0.0602 AC: 639 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0368 AC: 2500 AN: 68016

Other (OTH) AF: 0.0876 AC: 185 AN: 2112

Alfa AF: 0.0206 Hom.: 13

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.043
DANN	Benign	0.44
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs17158139; hg19: chr10-2362113;