chr10-61147427-T-A

Variant names:

• chr10-61147427-T-A
• rs7896712
• ENST00000687498.2:n.177-46545T>A

Variant summary

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

The ENST00000687498.2(LINC00845):​n.177-46545T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,678 control chromosomes in the GnomAD database, including 26,533 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 0.59 (26533 hom., cov: 30)
• Consequence: LINC00845 ENST00000687498.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 3 publications found

Genes affected

LINC00845 (HGNC:45033): (long intergenic non-protein coding RNA 845)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00845	ENST00000687498.2	n.177-46545T>A		intron_variant	Intron 1 of 1
LINC00845	ENST00000756399.1	n.544-10393T>A		intron_variant	Intron 4 of 4
LINC00845	ENST00000756400.1	n.479+24052T>A		intron_variant	Intron 3 of 3
LINC00845	ENST00000756403.1	n.74-10393T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89013 AN: 151562 Hom.: 26519 Cov.: 30

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.587 AC: 89073 AN: 151678 Hom.: 26533 Cov.: 30 AF XY: 0.583 AC XY: 43206 AN XY: 74086

African (AFR) AF: 0.617 AC: 25484 AN: 41336

American (AMR) AF: 0.641 AC: 9772 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1849 AN: 3466

East Asian (EAS) AF: 0.745 AC: 3810 AN: 5116

South Asian (SAS) AF: 0.669 AC: 3213 AN: 4802

European-Finnish (FIN) AF: 0.402 AC: 4227 AN: 10510

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38732 AN: 67888

Other (OTH) AF: 0.597 AC: 1259 AN: 2108

Alfa AF: 0.561 Hom.: 2875

Bravo AF: 0.607

Asia WGS AF: 0.715 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7896712; hg19: chr10-62907185;