rs11069790

Variant names:

• chr13-109592054-G-A
• rs11069790
• XR_007063870.1:n.1235C>T

Variant summary

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

The XR_007063870.1(LOC124903210):​n.1235C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 152,184 control chromosomes in the GnomAD database, including 826 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 0.085 (826 hom., cov: 33)
• Consequence: LOC124903210 XR_007063870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 2 publications found

Genes affected

LOC124903210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.1235C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LOC101927627	XR_007063867.1	n.77+1536G>A		intron_variant	Intron 1 of 3
LOC101927627	XR_007063868.1	n.129+725G>A		intron_variant	Intron 2 of 4
LOC101927627	XR_007063869.1	n.77+1536G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285534	ENST00000650264.1	n.759-20896C>T		intron_variant	Intron 1 of 3
ENSG00000296995	ENST00000744136.1	n.227+1536G>A		intron_variant	Intron 1 of 4
ENSG00000296995	ENST00000744137.1	n.287+725G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12929 AN: 152066 Hom.: 822 Cov.: 33

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0837

Gnomad OTH AF: 0.0942

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

GnomAD4 genome AF: 0.0850 AC: 12931 AN: 152184 Hom.: 826 Cov.: 33 AF XY: 0.0880 AC XY: 6551 AN XY: 74416

African (AFR) AF: 0.0325 AC: 1348 AN: 41518

American (AMR) AF: 0.119 AC: 1812 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3472

East Asian (EAS) AF: 0.285 AC: 1474 AN: 5170

South Asian (SAS) AF: 0.180 AC: 871 AN: 4832

European-Finnish (FIN) AF: 0.0703 AC: 745 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0837 AC: 5688 AN: 67992

Other (OTH) AF: 0.0946 AC: 200 AN: 2114

Alfa AF: 0.0835 Hom.: 1007

Bravo AF: 0.0880

Asia WGS AF: 0.225 AC: 779 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.042
DANN	Benign	0.41
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11069790; hg19: chr13-110244401;