13-20324191-T-A

Variant names:

• chr13-20324191-T-A
• rs11616264
• XR_941720.2:n.201-1174T>A

Variant summary

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

The XR_941720.2(LOC105370102):​n.201-1174T>A 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 151,918 control chromosomes in the GnomAD database, including 3,549 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 (3549 hom., cov: 31)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370102	XR_941720.2	n.201-1174T>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29149 AN: 151800 Hom.: 3558 Cov.: 31

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.192 AC: 29127 AN: 151918 Hom.: 3549 Cov.: 31 AF XY: 0.200 AC XY: 14837 AN XY: 74262

African (AFR) AF: 0.0514 AC: 2132 AN: 41474

American (AMR) AF: 0.196 AC: 2988 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3468

East Asian (EAS) AF: 0.426 AC: 2187 AN: 5132

South Asian (SAS) AF: 0.316 AC: 1517 AN: 4804

European-Finnish (FIN) AF: 0.261 AC: 2754 AN: 10540

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

European-Non Finnish (NFE) AF: 0.231 AC: 15707 AN: 67938

Other (OTH) AF: 0.202 AC: 426 AN: 2106

Alfa AF: 0.201 Hom.: 373

Bravo AF: 0.181

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.74
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11616264; hg19: chr13-20898330;