rs17089462

Variant names:

• chr13-64645041-G-A
• rs17089462
• XR_001750010.1:n.84+722G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-64645041-G-A
• chr13-64645041-G-T

Variant summary

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

The XR_001750010.1(LOC107987190):​n.84+722G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 152,150 control chromosomes in the GnomAD database, including 532 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 0.075 (532 hom., cov: 32)
• Consequence: LOC107987190 XR_001750010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 0 publications found

Genes affected

LOC107987190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11455 AN: 152032 Hom.: 528 Cov.: 32

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0180

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0836

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

GnomAD4 genome AF: 0.0754 AC: 11473 AN: 152150 Hom.: 532 Cov.: 32 AF XY: 0.0746 AC XY: 5549 AN XY: 74376

African (AFR) AF: 0.0330 AC: 1369 AN: 41532

American (AMR) AF: 0.0592 AC: 904 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 352 AN: 3466

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5162

South Asian (SAS) AF: 0.144 AC: 694 AN: 4826

European-Finnish (FIN) AF: 0.0923 AC: 977 AN: 10582

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

European-Non Finnish (NFE) AF: 0.100 AC: 6798 AN: 67988

Other (OTH) AF: 0.0884 AC: 187 AN: 2116

Alfa AF: 0.0372 Hom.: 41

Bravo AF: 0.0684

Asia WGS AF: 0.100 AC: 347 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.60
DANN	Benign	0.20
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs17089462; hg19: chr13-65219173; COSMIC: COSV60729873;