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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986634	XR_001744300.1	n.59+33488C>T		intron_variant	Intron 1 of 6
LOC107986634	XR_001744301.2	n.59+33488C>T		intron_variant	Intron 1 of 5
LOC107986634	XR_001744302.1	n.59+33488C>T		intron_variant	Intron 1 of 6
LOC107986634	XR_001744303.1	n.59+33488C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;