rs11238510

Variant names:

• chr10-43317737-C-T
• rs11238510
• ENST00000740943.1:n.160C>T

Variant summary

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

The ENST00000740943.1(LINC02633):​n.160C>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 0.0441 in 152,262 control chromosomes in the GnomAD database, including 272 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 0.044 (272 hom., cov: 32)
• Consequence: LINC02633 ENST00000740943.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 1 publications found

Genes affected

LINC02633 (HGNC:54116): (long intergenic non-protein coding RNA 2633)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 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
LINC02633	ENST00000740943.1	n.160C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0439 AC: 6674 AN: 152144 Hom.: 264 Cov.: 32

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0441 AC: 6716 AN: 152262 Hom.: 272 Cov.: 32 AF XY: 0.0465 AC XY: 3465 AN XY: 74462

African (AFR) AF: 0.0838 AC: 3481 AN: 41528

American (AMR) AF: 0.0704 AC: 1077 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0204 AC: 71 AN: 3472

East Asian (EAS) AF: 0.154 AC: 796 AN: 5184

South Asian (SAS) AF: 0.0558 AC: 269 AN: 4822

European-Finnish (FIN) AF: 0.0200 AC: 212 AN: 10624

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0104 AC: 710 AN: 68024

Other (OTH) AF: 0.0402 AC: 85 AN: 2114

Alfa AF: 0.0236 Hom.: 87

Bravo AF: 0.0505

Asia WGS AF: 0.102 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs11238510; hg19: chr10-43813185;