rs7163702

Variant names:

• chr15-28460135-C-A
• rs7163702
• XR_007064495.1:n.305-2334G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-28460135-C-A
• chr15-28460135-C-G
• chr15-28460135-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The XR_007064495.1(LOC101059997):​n.305-2334G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 (12204 hom., cov: 60)
  • Failed GnomAD Quality Control
• Consequence: LOC101059997 XR_007064495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 2 publications found

Genes affected

LOC101059997 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87219 AN: 151570 Hom.: 12150 Cov.: 60

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.545

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.576 AC: 87331 AN: 151688 Hom.: 12204 Cov.: 60 AF XY: 0.575 AC XY: 42602 AN XY: 74140

African (AFR) AF: 0.738 AC: 30621 AN: 41502

American (AMR) AF: 0.530 AC: 8066 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3464

East Asian (EAS) AF: 0.739 AC: 3834 AN: 5186

South Asian (SAS) AF: 0.551 AC: 2647 AN: 4806

European-Finnish (FIN) AF: 0.493 AC: 5183 AN: 10518

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33456 AN: 67692

Other (OTH) AF: 0.547 AC: 1151 AN: 2106

Alfa AF: 0.547 Hom.: 913

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.31
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7163702; hg19: chr15-28705281;