rs17602038

Variant names:

• chr11-113493969-T-C
• rs17602038
• XR_948024.2:n.107-2779A>G

Variant summary

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

The XR_948024.2(LOC105369501):​n.107-2779A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,036 control chromosomes in the GnomAD database, including 6,414 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 0.27 (6414 hom., cov: 32)
• Consequence: LOC105369501 XR_948024.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 9 publications found

Genes affected

LOC105369501 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 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: 0.266 AC: 40419 AN: 151918 Hom.: 6417 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.266 AC: 40405 AN: 152036 Hom.: 6414 Cov.: 32 AF XY: 0.256 AC XY: 19025 AN XY: 74324

African (AFR) AF: 0.124 AC: 5152 AN: 41500

American (AMR) AF: 0.308 AC: 4699 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1506 AN: 3466

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5174

South Asian (SAS) AF: 0.243 AC: 1167 AN: 4804

European-Finnish (FIN) AF: 0.177 AC: 1873 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24821 AN: 67946

Other (OTH) AF: 0.330 AC: 696 AN: 2106

Alfa AF: 0.322 Hom.: 14588

Bravo AF: 0.273

Asia WGS AF: 0.131 AC: 457 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.7
DANN	Benign	0.79
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs17602038; hg19: chr11-113364691;