6-130629904-A-G

Variant names:

• chr6-130629904-A-G
• rs9321244

Variant summary

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

The variant allele was found at a frequency of 0.0881 in 152,138 control chromosomes in the GnomAD database, including 886 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 0.088 (886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 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: 0.0880 AC: 13379 AN: 152018 Hom.: 878 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0590

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.0881 AC: 13408 AN: 152138 Hom.: 886 Cov.: 32 AF XY: 0.0943 AC XY: 7017 AN XY: 74388

African (AFR) AF: 0.0373 AC: 1551 AN: 41532

American (AMR) AF: 0.170 AC: 2598 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0590 AC: 205 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1286 AN: 5180

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4826

European-Finnish (FIN) AF: 0.0932 AC: 986 AN: 10584

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

European-Non Finnish (NFE) AF: 0.0768 AC: 5221 AN: 67978

Other (OTH) AF: 0.0992 AC: 209 AN: 2106

Alfa AF: 0.0873 Hom.: 80

Bravo AF: 0.0887

Asia WGS AF: 0.267 AC: 927 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs9321244; hg19: chr6-130951049;