6-112761302-A-G

Variant names:

• chr6-112761302-A-G
• rs10499068
• XR_001744300.1:n.188+8154T>C

Variant summary

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

The XR_001744300.1(LOC107986634):​n.188+8154T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,160 control chromosomes in the GnomAD database, including 978 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 0.10 (978 hom., cov: 32)
• Consequence: LOC107986634 XR_001744300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 2 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=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 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: 0.100 AC: 15239 AN: 152042 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.100 AC: 15239 AN: 152160 Hom.: 978 Cov.: 32 AF XY: 0.101 AC XY: 7545 AN XY: 74390

African (AFR) AF: 0.0214 AC: 891 AN: 41560

American (AMR) AF: 0.0859 AC: 1311 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3470

East Asian (EAS) AF: 0.102 AC: 530 AN: 5182

South Asian (SAS) AF: 0.0883 AC: 426 AN: 4826

European-Finnish (FIN) AF: 0.164 AC: 1733 AN: 10596

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9352 AN: 67946

Other (OTH) AF: 0.108 AC: 227 AN: 2110

Alfa AF: 0.119 Hom.: 162

Bravo AF: 0.0908

Asia WGS AF: 0.0740 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.92
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs10499068; hg19: chr6-113082504;