rs7900896

chr10-43812552-G-Achr10-43812552-G-Cchr10-43812552-G-T

Variant summary

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

The ENST00000659335.1(LINC00840):n.1025+15680G>A 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 0.356 in 151,910 control chromosomes in the GnomAD database, including 10,240 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 (10240 hom., cov: 31)
• Consequence: LINC00840 ENST00000659335.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

LINC00840 (HGNC:44987): (long intergenic non-protein coding RNA 840)

LOC105378275 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378275	XR_945906.4	n.1026-5955G>A		intron_variant, non_coding_transcript_variant
LOC105378275	XR_945907.2	n.179-5955G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00840	ENST00000659335.1	n.1025+15680G>A		intron_variant, non_coding_transcript_variant
LINC00840	ENST00000666323.1	n.1010+15680G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53947 AN: 151792 Hom.: 10205 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.356 AC: 54023 AN: 151910 Hom.: 10240 Cov.: 31 AF XY: 0.348 AC XY: 25855 AN XY: 74236

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.342

Alfa AF: 0.323 Hom.: 12352

Bravo AF: 0.371

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.6
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7900896; hg19: chr10-44308000;