rs7900896

Variant names:

• chr10-43812552-G-A
• rs7900896
• ENST00000659335.1:n.1025+15680G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-43812552-G-A
• chr10-43812552-G-C
• chr10-43812552-G-T

Variant summary

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

The ENST00000659335.1(LINC00840):​n.1025+15680G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 3 publications found

Genes affected

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

LOC105378275 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659335.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00840	ENST00000659335.1		n.1025+15680G>A		intron	N/A
	LINC00840	ENST00000666323.1		n.1010+15680G>A		intron	N/A
	LINC00840	ENST00000826488.1		n.262+15680G>A		intron	N/A

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

African (AFR) AF: 0.481 AC: 19926 AN: 41388

American (AMR) AF: 0.288 AC: 4402 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3466

East Asian (EAS) AF: 0.355 AC: 1827 AN: 5144

South Asian (SAS) AF: 0.224 AC: 1075 AN: 4804

European-Finnish (FIN) AF: 0.232 AC: 2446 AN: 10558

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22039 AN: 67958

Other (OTH) AF: 0.342 AC: 723 AN: 2114

Alfa AF: 0.336 Hom.: 20979

Bravo AF: 0.371

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7900896; hg19: chr10-44308000;