rs7896712

Positions:

• chr10-61147427-T-A
• chr10-61147427-T-C
• chr10-61147427-T-G

Variant summary

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

The ENST00000687498.1(LINC00845):​n.132-46545T>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 0.587 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 ENST00000687498.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00845	ENST00000687498.1	n.132-46545T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.597

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7896712; hg19: chr10-62907185;