rs10782174

Positions:

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

Variant summary

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

The XR_001744301.2(LOC107986634):​n.59+33488C>T variant causes a intron, non coding transcript 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_001744301.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

LOC107986634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107986634	XR_001744301.2	n.59+33488C>T		intron_variant, non_coding_transcript_variant
LOC107986634	XR_001744300.1	n.59+33488C>T		intron_variant, non_coding_transcript_variant
LOC107986634	XR_001744302.1	n.59+33488C>T		intron_variant, non_coding_transcript_variant
LOC107986634	XR_001744303.1	n.59+33488C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.878

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.822

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

Publications

LitVar

Other links and lift over

dbSNP: rs10782174; hg19: chr6-113134476;