rs2224536

Variant names:

• chr20-40027058-C-T
• rs2224536
• ENST00000423153.2:n.309-3667C>T

Variant summary

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

The ENST00000423153.2(LINC01370):​n.309-3667C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,070 control chromosomes in the GnomAD database, including 21,607 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 0.50 (21607 hom., cov: 32)
• Consequence: LINC01370 ENST00000423153.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 2 publications found

Genes affected

LINC01370 (HGNC:50608): (long intergenic non-protein coding RNA 1370)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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
LINC01370	ENST00000423153.2	n.309-3667C>T		intron_variant	Intron 2 of 5	3
LINC01370	ENST00000716850.1	n.309-7103C>T		intron_variant	Intron 2 of 3
LINC01370	ENST00000722236.1	n.309-3667C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75899 AN: 151952 Hom.: 21606 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.499 AC: 75895 AN: 152070 Hom.: 21607 Cov.: 32 AF XY: 0.499 AC XY: 37090 AN XY: 74296

African (AFR) AF: 0.219 AC: 9102 AN: 41508

American (AMR) AF: 0.562 AC: 8589 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1535 AN: 3470

East Asian (EAS) AF: 0.571 AC: 2945 AN: 5156

South Asian (SAS) AF: 0.476 AC: 2291 AN: 4818

European-Finnish (FIN) AF: 0.646 AC: 6819 AN: 10562

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42905 AN: 67968

Other (OTH) AF: 0.488 AC: 1030 AN: 2112

Alfa AF: 0.582 Hom.: 44925

Bravo AF: 0.480

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs2224536; hg19: chr20-38655700;