rs2075417

Positions:

• chr19-31990438-G-A

Variant summary

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

The XR_007067222.1(LINC01837):​n.254+19986C>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 0.388 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 XR_007067222.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01837	XR_007067222.1	n.254+19986C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01837	ENST00000590021.2	n.105-22805C>T		intron_variant, non_coding_transcript_variant		5
LINC01837	ENST00000590053.1	n.112+20084C>T		intron_variant, non_coding_transcript_variant		3
LINC01837	ENST00000593082.3	n.556+10159C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.384

Alfa AF: 0.373 Hom.: 1591

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2075417; hg19: chr19-32481344;