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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428766.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02935	ENST00000428766.3	TSL:5	n.420-14033T>C		intron	N/A
	LINC02935	ENST00000785198.1		n.418-17213T>C		intron	N/A
	LINC02935	ENST00000785199.1		n.189-14033T>C		intron	N/A

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 v4.9

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;