6-93182694-T-G

Variant names:

• chr6-93182694-T-G
• rs6901416

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.31 in 151,920 control chromosomes in the GnomAD database, including 8,561 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 0.31 (8561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 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: 0.310 AC: 47133 AN: 151802 Hom.: 8544 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.310 AC: 47170 AN: 151920 Hom.: 8561 Cov.: 32 AF XY: 0.304 AC XY: 22548 AN XY: 74260

African (AFR) AF: 0.512 AC: 21193 AN: 41414

American (AMR) AF: 0.215 AC: 3276 AN: 15236

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

East Asian (EAS) AF: 0.166 AC: 856 AN: 5152

South Asian (SAS) AF: 0.164 AC: 792 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2145 AN: 10580

Middle Eastern (MID) AF: 0.290 AC: 84 AN: 290

European-Non Finnish (NFE) AF: 0.250 AC: 16985 AN: 67938

Other (OTH) AF: 0.294 AC: 619 AN: 2108

Alfa AF: 0.233 Hom.: 2179

Bravo AF: 0.321

Asia WGS AF: 0.179 AC: 622 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.76
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6901416; hg19: chr6-93892412; COSMIC: COSV60247809;