10-61147270-A-C

Position:

• chr10-61147270-A-C

Variant summary

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

The ENST00000687498.1(LINC00845):​n.132-46702A>C 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 151,952 control chromosomes in the GnomAD database, including 26,556 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 (26556 hom., cov: 33)
• Consequence: LINC00845 ENST00000687498.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

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=-1.01).
• 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.132-46702A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89117 AN: 151834 Hom.: 26542 Cov.: 33

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.570

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: 89178 AN: 151952 Hom.: 26556 Cov.: 33 AF XY: 0.583 AC XY: 43275 AN XY: 74264

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.597

Alfa AF: 0.584 Hom.: 20354

Bravo AF: 0.607

Asia WGS AF: 0.714 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10761571; hg19: chr10-62907028;