2-241919597-C-T

Variant names:

• chr2-241919597-C-T
• rs4973665
• ENST00000415434.5:n.189+36962C>T

Variant summary

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

The ENST00000415434.5(LINC01237):​n.189+36962C>T variant causes a intron 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 ENST00000415434.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415434.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01237	NR_110220.1		n.192+36962C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01237	ENST00000415434.5	TSL:4	n.189+36962C>T		intron	N/A
	LINC01237	ENST00000429947.1	TSL:4	n.259-14477C>T		intron	N/A
	LINC01237	ENST00000430555.5	TSL:4	n.193-14477C>T		intron	N/A

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

African (AFR) AF: 0.0246 AC: 1018 AN: 41458

American (AMR) AF: 0.184 AC: 2809 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0122 AC: 42 AN: 3440

East Asian (EAS) AF: 0.481 AC: 2484 AN: 5166

South Asian (SAS) AF: 0.0952 AC: 451 AN: 4736

European-Finnish (FIN) AF: 0.0725 AC: 763 AN: 10518

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.0150 AC: 1013 AN: 67726

Other (OTH) AF: 0.0706 AC: 148 AN: 2096

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4973665;

hg19: chr2-242861748;