chr6-32709375-G-A

Variant names:

• chr6-32709375-G-A
• rs16898264

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 0.346 in 151,776 control chromosomes in the GnomAD database, including 9,458 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 0.35 (9458 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 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: 0.347 AC: 52561 AN: 151658 Hom.: 9460 Cov.: 30

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.346 AC: 52574 AN: 151776 Hom.: 9458 Cov.: 30 AF XY: 0.341 AC XY: 25258 AN XY: 74166

African (AFR) AF: 0.340 AC: 14050 AN: 41326

American (AMR) AF: 0.343 AC: 5230 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1552 AN: 3464

East Asian (EAS) AF: 0.422 AC: 2186 AN: 5176

South Asian (SAS) AF: 0.468 AC: 2245 AN: 4798

European-Finnish (FIN) AF: 0.190 AC: 1997 AN: 10532

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.353 AC: 23995 AN: 67902

Other (OTH) AF: 0.397 AC: 839 AN: 2112

Alfa AF: 0.346 Hom.: 10879

Bravo AF: 0.357

Asia WGS AF: 0.477 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.62
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs16898264; hg19: chr6-32677152; COSMIC: COSV70582317;