XR_941720.2:n.201-1714T>C

Variant names:

• chr13-20323651-T-C
• rs13379006
• XR_941720.2:n.201-1714T>C

Variant summary

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

The XR_941720.2(LOC105370102):​n.201-1714T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,064 control chromosomes in the GnomAD database, including 3,550 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 0.19 (3550 hom., cov: 32)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 1 publications found

Genes affected

LOC105370102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 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: 0.192 AC: 29159 AN: 151946 Hom.: 3559 Cov.: 32

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.192 AC: 29138 AN: 152064 Hom.: 3550 Cov.: 32 AF XY: 0.200 AC XY: 14835 AN XY: 74304

African (AFR) AF: 0.0514 AC: 2132 AN: 41510

American (AMR) AF: 0.196 AC: 2986 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1111 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2193 AN: 5156

South Asian (SAS) AF: 0.315 AC: 1511 AN: 4796

European-Finnish (FIN) AF: 0.262 AC: 2768 AN: 10578

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15713 AN: 67974

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.213 Hom.: 769

Bravo AF: 0.181

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs13379006; hg19: chr13-20897790;