rs11069790

Positions:

• chr13-109592054-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124903210 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124903210	XR_007063870.1	n.1235C>T		non_coding_transcript_exon_variant	2/2
LOC101927627	XR_007063867.1	n.77+1536G>A		intron_variant, non_coding_transcript_variant
LOC101927627	XR_007063868.1	n.129+725G>A		intron_variant, non_coding_transcript_variant
LOC101927627	XR_007063869.1	n.77+1536G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650264.1	n.759-20896C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0325

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0703

Gnomad4 NFE AF: 0.0837

Gnomad4 OTH AF: 0.0946

Alfa AF: 0.0868 Hom.: 704

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11069790; hg19: chr13-110244401;