6-32998165-G-A

Variant names:

• chr6-32998165-G-A
• rs176248

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 0.348 in 151,936 control chromosomes in the GnomAD database, including 11,078 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 (11078 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.348 AC: 52821 AN: 151818 Hom.: 11071 Cov.: 31

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.348 AC: 52870 AN: 151936 Hom.: 11078 Cov.: 31 AF XY: 0.336 AC XY: 24961 AN XY: 74254

African (AFR) AF: 0.591 AC: 24493 AN: 41426

American (AMR) AF: 0.264 AC: 4026 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 887 AN: 3468

East Asian (EAS) AF: 0.179 AC: 923 AN: 5166

South Asian (SAS) AF: 0.170 AC: 820 AN: 4810

European-Finnish (FIN) AF: 0.236 AC: 2491 AN: 10558

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18246 AN: 67918

Other (OTH) AF: 0.340 AC: 715 AN: 2106

Alfa AF: 0.293 Hom.: 18927

Bravo AF: 0.361

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.12
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs176248; hg19: chr6-32965942;