rs10500968

Variant names:

• chr11-23801921-T-C
• rs10500968
• ENST00000525512.2:n.264+2558A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-23801921-T-C
• chr11-23801921-T-G

Variant summary

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

The ENST00000525512.2(ENSG00000254861):​n.264+2558A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0768 in 152,250 control chromosomes in the GnomAD database, including 1,097 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 0.077 (1097 hom., cov: 32)
• Consequence: ENSG00000254861 ENST00000525512.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 3 publications found

Genes affected

ENSG00000254861 (HGNC:):

LINC02726 (HGNC:54243): (long intergenic non-protein coding RNA 2726)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254861	ENST00000525512.2	n.264+2558A>G		intron_variant	Intron 2 of 3	3
LINC02726	ENST00000779955.1	n.395-20611T>C		intron_variant	Intron 2 of 2
ENSG00000254861	ENST00000780027.1	n.261+2558A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11677 AN: 152130 Hom.: 1096 Cov.: 32

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0768 AC: 11689 AN: 152250 Hom.: 1097 Cov.: 32 AF XY: 0.0812 AC XY: 6044 AN XY: 74434

African (AFR) AF: 0.0166 AC: 689 AN: 41576

American (AMR) AF: 0.162 AC: 2479 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2474 AN: 5152

South Asian (SAS) AF: 0.138 AC: 664 AN: 4822

European-Finnish (FIN) AF: 0.0650 AC: 691 AN: 10624

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0645 AC: 4388 AN: 68014

Other (OTH) AF: 0.0795 AC: 168 AN: 2114

Alfa AF: 0.0751 Hom.: 656

Bravo AF: 0.0867

Asia WGS AF: 0.301 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.50
DANN	Benign	0.62
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10500968; hg19: chr11-23823467;