rs7911302

Variant names:

• chr10-61147468-A-C
• rs7911302
• ENST00000687498.1:n.132-46504A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-61147468-A-C
• chr10-61147468-A-T

Variant summary

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

The ENST00000687498.1(LINC00845):​n.132-46504A>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 ENST00000687498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

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=-0.89).
• 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	ENST00000687498.1	n.132-46504A>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

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.564

Alfa AF: 0.562 Hom.: 46778

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7911302; hg19: chr10-62907226;