rs1695718

Variant names:

• chr8-117377370-C-T
• rs1695718
• XR_007061067.1:n.559+63590G>A

Variant summary

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

The XR_928568.4(LOC105375716):​n.714+63590G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,774 control chromosomes in the GnomAD database, including 4,064 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 0.20 (4064 hom., cov: 32)
• Consequence: LOC105375716 XR_928568.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 1 publications found

Genes affected

LOC105375716 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

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: 0.205 AC: 31105 AN: 151656 Hom.: 4065 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.205 AC: 31088 AN: 151774 Hom.: 4064 Cov.: 32 AF XY: 0.205 AC XY: 15194 AN XY: 74172

African (AFR) AF: 0.0579 AC: 2389 AN: 41296

American (AMR) AF: 0.136 AC: 2073 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1660 AN: 5142

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4808

European-Finnish (FIN) AF: 0.291 AC: 3068 AN: 10552

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19384 AN: 67980

Other (OTH) AF: 0.194 AC: 409 AN: 2108

Alfa AF: 0.265 Hom.: 4922

Bravo AF: 0.187

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.63
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1695718; hg19: chr8-118389609;