rs3105764

Variant names:

• chr8-117722487-T-A
• rs3105764
• XR_007061071.1:n.9653A>T

Your query was ambiguous. Multiple possible variants found:

• chr8-117722487-T-A
• chr8-117722487-T-C
• chr8-117722487-T-G

Variant summary

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

The XR_007061071.1(LOC105375721):​n.9653A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,058 control chromosomes in the GnomAD database, including 37,724 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 0.69 (37724 hom., cov: 32)
• Consequence: LOC105375721 XR_007061071.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 0 publications found

Genes affected

LOC105375721 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 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: 0.692 AC: 105132 AN: 151940 Hom.: 37676 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.692 AC: 105239 AN: 152058 Hom.: 37724 Cov.: 32 AF XY: 0.691 AC XY: 51309 AN XY: 74304

African (AFR) AF: 0.896 AC: 37195 AN: 41502

American (AMR) AF: 0.592 AC: 9045 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2098 AN: 3468

East Asian (EAS) AF: 0.718 AC: 3705 AN: 5158

South Asian (SAS) AF: 0.680 AC: 3272 AN: 4812

European-Finnish (FIN) AF: 0.623 AC: 6583 AN: 10564

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41266 AN: 67956

Other (OTH) AF: 0.631 AC: 1330 AN: 2108

Alfa AF: 0.661 Hom.: 4223

Bravo AF: 0.696

Asia WGS AF: 0.678 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.23
DANN	Benign	0.68
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3105764; hg19: chr8-118734726;