rs11196152

Variant names:

• chr10-112927046-T-C
• rs11196152
• ENST00000428766.3:n.420-14033T>C

Variant summary

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

The ENST00000428766.3(LINC02935):​n.420-14033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,052 control chromosomes in the GnomAD database, including 18,786 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 0.49 (18786 hom., cov: 32)
• Consequence: LINC02935 ENST00000428766.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 7 publications found

Genes affected

LINC02935 (HGNC:55939): (long intergenic non-protein coding RNA 2935)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02935	XR_001747706.2	n.279-83T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02935	ENST00000428766.3	n.420-14033T>C		intron_variant	Intron 3 of 7	5
LINC02935	ENST00000785198.1	n.418-17213T>C		intron_variant	Intron 3 of 3
LINC02935	ENST00000785199.1	n.189-14033T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74469 AN: 151934 Hom.: 18764 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.490 AC: 74536 AN: 152052 Hom.: 18786 Cov.: 32 AF XY: 0.483 AC XY: 35878 AN XY: 74342

African (AFR) AF: 0.518 AC: 21467 AN: 41470

American (AMR) AF: 0.489 AC: 7466 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1761 AN: 3468

East Asian (EAS) AF: 0.0655 AC: 339 AN: 5176

South Asian (SAS) AF: 0.370 AC: 1782 AN: 4816

European-Finnish (FIN) AF: 0.469 AC: 4963 AN: 10572

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 34999 AN: 67964

Other (OTH) AF: 0.509 AC: 1075 AN: 2112

Alfa AF: 0.498 Hom.: 84041

Bravo AF: 0.488

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.1
DANN	Benign	0.76
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11196152; hg19: chr10-114686805;