10-61147197-T-G

Variant names:

• chr10-61147197-T-G
• rs10761570
• ENST00000687498.2:n.177-46775T>G

Variant summary

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

The ENST00000687498.2(LINC00845):​n.177-46775T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,962 control chromosomes in the GnomAD database, including 21,455 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 0.52 (21455 hom., cov: 32)
• Consequence: LINC00845 ENST00000687498.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 2 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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.177-46775T>G		intron_variant	Intron 1 of 1
LINC00845	ENST00000756399.1	n.544-10623T>G		intron_variant	Intron 4 of 4
LINC00845	ENST00000756400.1	n.479+23822T>G		intron_variant	Intron 3 of 3
LINC00845	ENST00000756403.1	n.74-10623T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79351 AN: 151844 Hom.: 21450 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.522 AC: 79392 AN: 151962 Hom.: 21455 Cov.: 32 AF XY: 0.520 AC XY: 38656 AN XY: 74276

African (AFR) AF: 0.421 AC: 17462 AN: 41450

American (AMR) AF: 0.617 AC: 9398 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3832 AN: 5156

South Asian (SAS) AF: 0.666 AC: 3212 AN: 4820

European-Finnish (FIN) AF: 0.387 AC: 4095 AN: 10574

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.555 AC: 37712 AN: 67952

Other (OTH) AF: 0.547 AC: 1153 AN: 2108

Alfa AF: 0.536 Hom.: 11561

Bravo AF: 0.536

Asia WGS AF: 0.701 AC: 2433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.1
DANN	Benign	0.76
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10761570; hg19: chr10-62906955;