rs4640436

Positions:

• chr2-42975024-G-A
• chr2-42975024-G-T

Variant summary

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

The ENST00000705222.1(LINC01819):​n.773-2014C>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 0.359 in 152,062 control chromosomes in the GnomAD database, including 9,906 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 0.36 (9906 hom., cov: 32)
• Consequence: LINC01819 ENST00000705222.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51

Genes affected

LINC01819 (HGNC:52624): (long intergenic non-protein coding RNA 1819)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01819	ENST00000705222.1	n.773-2014C>T		intron_variant, non_coding_transcript_variant
LINC01819	ENST00000705221.1	n.456-2014C>T		intron_variant, non_coding_transcript_variant
LINC01819	ENST00000705223.1	n.258+1213C>T		intron_variant, non_coding_transcript_variant
LINC01819	ENST00000705224.1	n.596-2014C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54549 AN: 151944 Hom.: 9902 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.359 AC: 54571 AN: 152062 Hom.: 9906 Cov.: 32 AF XY: 0.356 AC XY: 26483 AN XY: 74332

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.380

Alfa AF: 0.208 Hom.: 467

Bravo AF: 0.356

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.26
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4640436; hg19: chr2-43202164;