13-20324177-T-C

Variant names:

• chr13-20324177-T-C
• rs9509139
• XR_941720.2:n.201-1188T>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.201-1188T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,802 control chromosomes in the GnomAD database, including 13,330 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 0.39 (13330 hom., cov: 31)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 0 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370102	XR_941720.2	n.201-1188T>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58575 AN: 151682 Hom.: 13324 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.386 AC: 58597 AN: 151802 Hom.: 13330 Cov.: 31 AF XY: 0.384 AC XY: 28479 AN XY: 74168

African (AFR) AF: 0.140 AC: 5795 AN: 41424

American (AMR) AF: 0.430 AC: 6570 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1201 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1268 AN: 5142

South Asian (SAS) AF: 0.440 AC: 2116 AN: 4806

European-Finnish (FIN) AF: 0.494 AC: 5208 AN: 10540

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34950 AN: 67858

Other (OTH) AF: 0.399 AC: 838 AN: 2100

Alfa AF: 0.441 Hom.: 2025

Bravo AF: 0.369

Asia WGS AF: 0.395 AC: 1377 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	5.7
DANN	Benign	0.83
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9509139; hg19: chr13-20898316;