chr3-52810518-C-T

Variant names:

• chr3-52810518-C-T
• rs17331151
• XR_007095911.1:n.103G>A

Variant summary

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

The XR_007095911.1(LOC124906240):​n.103G>A 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 0.0753 in 152,240 control chromosomes in the GnomAD database, including 565 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 (565 hom., cov: 32)
• Consequence: LOC124906240 XR_007095911.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 27 publications found

Genes affected

LOC124906240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 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: 11458 AN: 152120 Hom.: 564 Cov.: 32

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0508

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0753 AC: 11461 AN: 152240 Hom.: 565 Cov.: 32 AF XY: 0.0722 AC XY: 5375 AN XY: 74448

African (AFR) AF: 0.0204 AC: 849 AN: 41548

American (AMR) AF: 0.0934 AC: 1429 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3472

East Asian (EAS) AF: 0.0509 AC: 263 AN: 5168

South Asian (SAS) AF: 0.0342 AC: 165 AN: 4826

European-Finnish (FIN) AF: 0.0733 AC: 778 AN: 10612

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7324 AN: 67996

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.102 Hom.: 3726

Bravo AF: 0.0760

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.32
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs17331151; hg19: chr3-52844534;