rs11616264

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-20324191-T-A
• chr13-20324191-T-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.201-1174T>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.

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: 0.192 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 v4.9

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;