rs2434772

Variant names:

• chr5-20615971-C-T
• rs2434772
• ENST00000655312.1:n.208C>T

Variant summary

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

The ENST00000655312.1(LINC02241):​n.208C>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 0.376 in 151,928 control chromosomes in the GnomAD database, including 11,412 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 0.38 (11412 hom., cov: 32)
• Consequence: LINC02241 ENST00000655312.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 1 publications found

Genes affected

LINC02241 (HGNC:53126): (long intergenic non-protein coding RNA 2241)

LINC02146 (HGNC:53006): (long intergenic non-protein coding RNA 2146)

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 (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02241	NR_149120.1	n.146+3986C>T		intron_variant	Intron 1 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02241	ENST00000655312.1	n.208C>T		non_coding_transcript_exon_variant	Exon 1 of 11
LINC02146	ENST00000659986.1	n.354G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LINC02241	ENST00000765452.1	n.258C>T		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57160 AN: 151812 Hom.: 11412 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.376 AC: 57177 AN: 151928 Hom.: 11412 Cov.: 32 AF XY: 0.374 AC XY: 27780 AN XY: 74246

African (AFR) AF: 0.247 AC: 10245 AN: 41442

American (AMR) AF: 0.388 AC: 5920 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1771 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1962 AN: 5152

South Asian (SAS) AF: 0.464 AC: 2234 AN: 4812

European-Finnish (FIN) AF: 0.381 AC: 4007 AN: 10526

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29621 AN: 67954

Other (OTH) AF: 0.407 AC: 858 AN: 2110

Alfa AF: 0.425 Hom.: 26632

Bravo AF: 0.372

Asia WGS AF: 0.387 AC: 1343 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	3.1
DANN	Benign	0.68
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs2434772; hg19: chr5-20616080;