rs17746501

Variant names:

• chr10-112889708-A-G
• rs17746501
• ENST00000428766.3:n.75+901A>G

Variant summary

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

The ENST00000428766.3(LINC02935):​n.75+901A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,032 control chromosomes in the GnomAD database, including 5,213 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 0.25 (5213 hom., cov: 32)
• Consequence: LINC02935 ENST00000428766.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 14 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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
LINC02935	ENST00000428766.3	n.75+901A>G		intron_variant	Intron 1 of 7	5
LINC02935	ENST00000785198.1	n.73+901A>G		intron_variant	Intron 1 of 3
LINC02935	ENST00000785199.1	n.81+901A>G		intron_variant	Intron 1 of 3
LINC02935	ENST00000785200.1	n.75+901A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38151 AN: 151912 Hom.: 5214 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.251 AC: 38162 AN: 152032 Hom.: 5213 Cov.: 32 AF XY: 0.250 AC XY: 18577 AN XY: 74334

African (AFR) AF: 0.200 AC: 8283 AN: 41456

American (AMR) AF: 0.227 AC: 3462 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1163 AN: 3468

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5174

South Asian (SAS) AF: 0.197 AC: 950 AN: 4820

European-Finnish (FIN) AF: 0.299 AC: 3159 AN: 10568

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20169 AN: 67960

Other (OTH) AF: 0.282 AC: 596 AN: 2114

Alfa AF: 0.264 Hom.: 829

Bravo AF: 0.242

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.71
DANN	Benign	0.85
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17746501; hg19: chr10-114649467;