6-32703201-A-G

Variant names:

• chr6-32703201-A-G
• rs9275428

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 0.295 in 151,928 control chromosomes in the GnomAD database, including 7,076 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 0.29 (7076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44755 AN: 151810 Hom.: 7060 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.295 AC: 44816 AN: 151928 Hom.: 7076 Cov.: 32 AF XY: 0.305 AC XY: 22655 AN XY: 74276

African (AFR) AF: 0.294 AC: 12186 AN: 41414

American (AMR) AF: 0.397 AC: 6064 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3466

East Asian (EAS) AF: 0.297 AC: 1540 AN: 5182

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4802

European-Finnish (FIN) AF: 0.467 AC: 4923 AN: 10550

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16931 AN: 67944

Other (OTH) AF: 0.288 AC: 607 AN: 2106

Alfa AF: 0.271 Hom.: 19581

Bravo AF: 0.295

Asia WGS AF: 0.277 AC: 969 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.4
DANN	Benign	0.79
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs9275428; hg19: chr6-32670978;