10-61147468-A-C

Variant names:

• chr10-61147468-A-C
• rs7911302
• ENST00000687498.2:n.177-46504A>C

Variant summary

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

The ENST00000687498.2(LINC00845):​n.177-46504A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,740 control chromosomes in the GnomAD database, including 23,020 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 0.55 (23020 hom., cov: 31)
• Consequence: LINC00845 ENST00000687498.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 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.177-46504A>C		intron_variant	Intron 1 of 1
LINC00845	ENST00000756399.1	n.544-10352A>C		intron_variant	Intron 4 of 4
LINC00845	ENST00000756400.1	n.479+24093A>C		intron_variant	Intron 3 of 3
LINC00845	ENST00000756403.1	n.74-10352A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82697 AN: 151622 Hom.: 23011 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.545 AC: 82749 AN: 151740 Hom.: 23020 Cov.: 31 AF XY: 0.542 AC XY: 40190 AN XY: 74100

African (AFR) AF: 0.502 AC: 20769 AN: 41346

American (AMR) AF: 0.624 AC: 9504 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1803 AN: 3466

East Asian (EAS) AF: 0.738 AC: 3770 AN: 5108

South Asian (SAS) AF: 0.667 AC: 3214 AN: 4818

European-Finnish (FIN) AF: 0.388 AC: 4088 AN: 10536

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37683 AN: 67908

Other (OTH) AF: 0.564 AC: 1193 AN: 2116

Alfa AF: 0.560 Hom.: 74246

Bravo AF: 0.562

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs7911302; hg19: chr10-62907226;