6-112803099-C-T

Variant names:

• chr6-112803099-C-T
• rs6934970
• XR_001744300.1:n.60-33515G>A

Variant summary

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

The XR_001744300.1(LOC107986634):​n.60-33515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 151,748 control chromosomes in the GnomAD database, including 51,268 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 0.82 (51268 hom., cov: 31)
• Consequence: LOC107986634 XR_001744300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 6 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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123711 AN: 151630 Hom.: 51253 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.816 AC: 123765 AN: 151748 Hom.: 51268 Cov.: 31 AF XY: 0.817 AC XY: 60619 AN XY: 74188

African (AFR) AF: 0.645 AC: 26722 AN: 41430

American (AMR) AF: 0.879 AC: 13389 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2924 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4633 AN: 5164

South Asian (SAS) AF: 0.917 AC: 4427 AN: 4830

European-Finnish (FIN) AF: 0.875 AC: 9255 AN: 10572

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

European-Non Finnish (NFE) AF: 0.881 AC: 59699 AN: 67746

Other (OTH) AF: 0.823 AC: 1732 AN: 2104

Alfa AF: 0.847 Hom.: 18664

Bravo AF: 0.806

Asia WGS AF: 0.902 AC: 3135 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs6934970; hg19: chr6-113124301;