6-119991183-G-T

Variant names:

• chr6-119991183-G-T
• rs9320730

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 0.267 in 151,970 control chromosomes in the GnomAD database, including 5,723 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 0.27 (5723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40569 AN: 151852 Hom.: 5720 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.267 AC: 40585 AN: 151970 Hom.: 5723 Cov.: 32 AF XY: 0.270 AC XY: 20079 AN XY: 74264

African (AFR) AF: 0.237 AC: 9805 AN: 41434

American (AMR) AF: 0.222 AC: 3386 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3468

East Asian (EAS) AF: 0.549 AC: 2833 AN: 5162

South Asian (SAS) AF: 0.374 AC: 1800 AN: 4814

European-Finnish (FIN) AF: 0.320 AC: 3381 AN: 10556

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17502 AN: 67952

Other (OTH) AF: 0.272 AC: 573 AN: 2108

Alfa AF: 0.260 Hom.: 4383

Bravo AF: 0.261

Asia WGS AF: 0.425 AC: 1476 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9320730; hg19: chr6-120312329;