rs2075417

Variant names:

• chr19-31990438-G-A
• rs2075417
• ENST00000590021.2:n.105-22805C>T

Variant summary

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

The ENST00000590021.2(LINC01837):​n.105-22805C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,128 control chromosomes in the GnomAD database, including 12,276 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 0.39 (12276 hom., cov: 33)
• Consequence: LINC01837 ENST00000590021.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 1 publications found

Genes affected

LINC01837 (HGNC:52653): (long intergenic non-protein coding RNA 1837)

ENSG00000303073 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01837	XR_001753904.2	n.226+19986C>T		intron_variant	Intron 2 of 13
LINC01837	XR_001753905.2	n.226+19986C>T		intron_variant	Intron 2 of 12
LINC01837	XR_001753907.2	n.226+19986C>T		intron_variant	Intron 2 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01837	ENST00000590021.2	n.105-22805C>T		intron_variant	Intron 2 of 3	5
LINC01837	ENST00000590053.1	n.112+20084C>T		intron_variant	Intron 2 of 2	3
LINC01837	ENST00000593082.3	n.556+10159C>T		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58952 AN: 152010 Hom.: 12258 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.388 AC: 59026 AN: 152128 Hom.: 12276 Cov.: 33 AF XY: 0.385 AC XY: 28634 AN XY: 74366

African (AFR) AF: 0.542 AC: 22493 AN: 41480

American (AMR) AF: 0.364 AC: 5568 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1261 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2346 AN: 5164

South Asian (SAS) AF: 0.340 AC: 1640 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2922 AN: 10586

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21462 AN: 68008

Other (OTH) AF: 0.384 AC: 811 AN: 2110

Alfa AF: 0.379 Hom.: 1708

Bravo AF: 0.406

Asia WGS AF: 0.408 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.021
DANN	Benign	0.66
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2075417; hg19: chr19-32481344;