rs852102

Variant names:

• chr20-17173740-G-A
• rs852102
• XR_937289.1:n.311-139G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-17173740-G-A
• chr20-17173740-G-C

Variant summary

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

The XR_937289.1(LOC105372544):​n.311-139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,206 control chromosomes in the GnomAD database, including 49,430 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 0.80 (49430 hom., cov: 33)
• Consequence: LOC105372544 XR_937289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 2 publications found

Genes affected

LOC105372544 (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 (NFE) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372544	XR_937289.1	n.311-139G>A		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121529 AN: 152088 Hom.: 49422 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.799 AC: 121565 AN: 152206 Hom.: 49430 Cov.: 33 AF XY: 0.795 AC XY: 59191 AN XY: 74422

African (AFR) AF: 0.685 AC: 28455 AN: 41522

American (AMR) AF: 0.716 AC: 10952 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3143 AN: 3472

East Asian (EAS) AF: 0.578 AC: 2983 AN: 5160

South Asian (SAS) AF: 0.747 AC: 3602 AN: 4820

European-Finnish (FIN) AF: 0.917 AC: 9725 AN: 10606

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60072 AN: 68018

Other (OTH) AF: 0.807 AC: 1706 AN: 2114

Alfa AF: 0.827 Hom.: 10300

Bravo AF: 0.777

Asia WGS AF: 0.645 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.26
DANN	Benign	0.72
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs852102; hg19: chr20-17154385;