3-52810518-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906240	XR_007095911.1	n.103G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;