rs10782174

Variant names:

• chr6-112813274-G-A
• rs10782174
• XR_001744300.1:n.59+33488C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-112813274-G-A
• chr6-112813274-G-C
• chr6-112813274-G-T

Variant summary

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

The XR_001744300.1(LOC107986634):​n.59+33488C>T variant causes a intron change. The variant allele was found at a frequency of 0.814 in 150,256 control chromosomes in the GnomAD database, including 50,530 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 0.81 (50530 hom., cov: 29)
• Consequence: LOC107986634 XR_001744300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 0 publications found

Genes affected

LOC107986634 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.815 AC: 122303 AN: 150138 Hom.: 50516 Cov.: 29

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.814 AC: 122353 AN: 150256 Hom.: 50530 Cov.: 29 AF XY: 0.816 AC XY: 59828 AN XY: 73346

African (AFR) AF: 0.646 AC: 26535 AN: 41058

American (AMR) AF: 0.878 AC: 13288 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2899 AN: 3444

East Asian (EAS) AF: 0.897 AC: 4535 AN: 5058

South Asian (SAS) AF: 0.913 AC: 4275 AN: 4682

European-Finnish (FIN) AF: 0.872 AC: 9096 AN: 10432

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59059 AN: 67190

Other (OTH) AF: 0.822 AC: 1693 AN: 2060

Alfa AF: 0.838 Hom.: 5422

Bravo AF: 0.805

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.1
DANN	Benign	0.97

Splicing

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

Other links and lift over

dbSNP: rs10782174; hg19: chr6-113134476;