rs17820943

Variant names:

• chr20-40639876-C-T
• rs17820943
• XR_001754596.2:n.165+658G>A

Variant summary

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

The XR_001754596.2(LOC102724968):​n.165+658G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,082 control chromosomes in the GnomAD database, including 10,244 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 0.36 (10244 hom., cov: 32)
• Consequence: LOC102724968 XR_001754596.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 14 publications found

Genes affected

LOC102724968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724968	XR_001754596.2	n.165+658G>A		intron_variant	Intron 2 of 7
LOC102724968	XR_001754597.1	n.180+4035G>A		intron_variant	Intron 1 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54962 AN: 151964 Hom.: 10252 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.361 AC: 54962 AN: 152082 Hom.: 10244 Cov.: 32 AF XY: 0.365 AC XY: 27107 AN XY: 74322

African (AFR) AF: 0.259 AC: 10768 AN: 41500

American (AMR) AF: 0.377 AC: 5769 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1753 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2303 AN: 5162

South Asian (SAS) AF: 0.387 AC: 1862 AN: 4816

European-Finnish (FIN) AF: 0.414 AC: 4367 AN: 10560

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27017 AN: 67972

Other (OTH) AF: 0.356 AC: 752 AN: 2110

Alfa AF: 0.387 Hom.: 21362

Bravo AF: 0.355

Asia WGS AF: 0.365 AC: 1272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.40
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs17820943; hg19: chr20-39268516;