6-129895365-A-G

Variant names:

• chr6-129895365-A-G
• rs9375674
• XR_942986.3:n.355+7292A>G

Variant summary

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

The XR_942986.3(LOC105377999):​n.355+7292A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,868 control chromosomes in the GnomAD database, including 21,241 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 0.53 (21241 hom., cov: 30)
• Consequence: LOC105377999 XR_942986.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54
• Publications: 12 publications found

Genes affected

LOC105377999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 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: 0.526 AC: 79816 AN: 151750 Hom.: 21218 Cov.: 30

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.526 AC: 79883 AN: 151868 Hom.: 21241 Cov.: 30 AF XY: 0.527 AC XY: 39101 AN XY: 74224

African (AFR) AF: 0.487 AC: 20153 AN: 41380

American (AMR) AF: 0.574 AC: 8773 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1510 AN: 3470

East Asian (EAS) AF: 0.657 AC: 3390 AN: 5162

South Asian (SAS) AF: 0.461 AC: 2214 AN: 4806

European-Finnish (FIN) AF: 0.550 AC: 5795 AN: 10542

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36586 AN: 67918

Other (OTH) AF: 0.504 AC: 1064 AN: 2110

Alfa AF: 0.534 Hom.: 77111

Bravo AF: 0.528

Asia WGS AF: 0.569 AC: 1979 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.081
DANN	Benign	0.72
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs9375674; hg19: chr6-130216510;