rs13041247

Variant names:

• chr20-40640434-T-C
• rs13041247
• XR_001754596.2:n.165+100A>G

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+100A>G 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 152,094 control chromosomes in the GnomAD database, including 10,235 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 (10235 hom., cov: 32)
• Consequence: LOC102724968 XR_001754596.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 56 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 = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724968	XR_001754596.2	n.165+100A>G		intron_variant	Intron 2 of 7
LOC102724968	XR_001754597.1	n.180+3477A>G		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: 54956 AN: 151976 Hom.: 10243 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.357

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: 54956 AN: 152094 Hom.: 10235 Cov.: 32 AF XY: 0.364 AC XY: 27105 AN XY: 74366

African (AFR) AF: 0.259 AC: 10761 AN: 41492

American (AMR) AF: 0.377 AC: 5763 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1751 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2312 AN: 5172

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4816

European-Finnish (FIN) AF: 0.413 AC: 4361 AN: 10572

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.397 AC: 27023 AN: 67986

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

Alfa AF: 0.383 Hom.: 23665

Bravo AF: 0.355

Asia WGS AF: 0.365 AC: 1273 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	6.7
DANN	Benign	0.79
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs13041247; hg19: chr20-39269074;