10-61067194-C-T

Position:

• chr10-61067194-C-T

Variant summary

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

The ENST00000687498.1(LINC00845):​n.131+65976C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,034 control chromosomes in the GnomAD database, including 37,134 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 0.69 (37134 hom., cov: 31)
• Consequence: LINC00845 ENST00000687498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

LINC00845 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902434	XR_007062154.1	n.48+699G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00845	ENST00000687498.1	n.131+65976C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104629 AN: 151914 Hom.: 37100 Cov.: 31

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.689 AC: 104718 AN: 152034 Hom.: 37134 Cov.: 31 AF XY: 0.683 AC XY: 50728 AN XY: 74312

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.681

Alfa AF: 0.651 Hom.: 46050

Bravo AF: 0.710

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7922793; hg19: chr10-62826952;