XR_001754597.1:n.180+1735G>A

Variant names:

• chr20-40642176-C-T
• rs11696257
• XR_001754597.1:n.180+1735G>A

Variant summary

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

The XR_001754597.1(LOC102724968):​n.180+1735G>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 152,160 control chromosomes in the GnomAD database, including 10,239 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 (10239 hom., cov: 33)
• Consequence: LOC102724968 XR_001754597.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 20 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

Selected	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: 54965 AN: 152042 Hom.: 10247 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.293

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: 0.360

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

GnomAD4 genome AF: 0.361 AC: 54963 AN: 152160 Hom.: 10239 Cov.: 33 AF XY: 0.365 AC XY: 27124 AN XY: 74386

African (AFR) AF: 0.259 AC: 10742 AN: 41520

American (AMR) AF: 0.377 AC: 5772 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1751 AN: 3466

East Asian (EAS) AF: 0.446 AC: 2306 AN: 5168

South Asian (SAS) AF: 0.386 AC: 1863 AN: 4828

European-Finnish (FIN) AF: 0.414 AC: 4380 AN: 10588

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

European-Non Finnish (NFE) AF: 0.398 AC: 27024 AN: 67980

Other (OTH) AF: 0.357 AC: 753 AN: 2110

Alfa AF: 0.368 Hom.: 5664

Bravo AF: 0.355

Asia WGS AF: 0.364 AC: 1270 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	2.3
DANN	Benign	0.79
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11696257; hg19: chr20-39270816;