2-241919597-C-T

Position:

• chr2-241919597-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110220.1(LINC01237):​n.192+36962C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0576 in 151,590 control chromosomes in the GnomAD database, including 1,156 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 0.058 (1156 hom., cov: 32)
• Consequence: LINC01237 NR_110220.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

LINC01237 (HGNC:49793): (long intergenic non-protein coding RNA 1237)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01237	NR_110220.1	n.192+36962C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01237	ENST00000415434.5	n.189+36962C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 8710 AN: 151472 Hom.: 1149 Cov.: 32

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0122

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.0725

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0665

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

GnomAD4 genome AF: 0.0576 AC: 8733 AN: 151590 Hom.: 1156 Cov.: 32 AF XY: 0.0668 AC XY: 4952 AN XY: 74082

Gnomad4 AFR AF: 0.0246

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0122

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.0952

Gnomad4 FIN AF: 0.0725

Gnomad4 NFE AF: 0.0150

Gnomad4 OTH AF: 0.0706

Alfa AF: 0.0124 Hom.: 11

Bravo AF: 0.0660

Asia WGS AF: 0.263 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4973665; hg19: chr2-242861748;