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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;