rs17746916

Variant names:

• chr10-112945022-C-T
• rs17746916
• ENST00000785201.1:n.871C>T

Variant summary

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

The ENST00000785201.1(LINC02935):​n.871C>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 0.0468 in 152,216 control chromosomes in the GnomAD database, including 223 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 0.047 (223 hom., cov: 32)
• Consequence: LINC02935 ENST00000785201.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0664 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	ENST00000785201.1	n.871C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02935	ENST00000428766.3	n.1041+223C>T		intron_variant	Intron 5 of 7	5
LINC02935	ENST00000785200.1	n.853+223C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 7118 AN: 152098 Hom.: 223 Cov.: 32

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0468 AC: 7119 AN: 152216 Hom.: 223 Cov.: 32 AF XY: 0.0464 AC XY: 3449 AN XY: 74412

African (AFR) AF: 0.0120 AC: 498 AN: 41528

American (AMR) AF: 0.0619 AC: 946 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 148 AN: 3468

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5192

South Asian (SAS) AF: 0.0355 AC: 171 AN: 4822

European-Finnish (FIN) AF: 0.0501 AC: 531 AN: 10592

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0681 AC: 4629 AN: 68010

Other (OTH) AF: 0.0601 AC: 127 AN: 2112

Alfa AF: 0.0651 Hom.: 605

Bravo AF: 0.0450

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.49
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs17746916; hg19: chr10-114704781;