6-32933010-C-T

Variant names:

• chr6-32933010-C-T
• rs3129299

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 0.236 in 152,094 control chromosomes in the GnomAD database, including 5,014 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 0.24 (5014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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: 0.236 AC: 35915 AN: 151976 Hom.: 5006 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.236 AC: 35940 AN: 152094 Hom.: 5014 Cov.: 32 AF XY: 0.234 AC XY: 17381 AN XY: 74346

African (AFR) AF: 0.367 AC: 15217 AN: 41428

American (AMR) AF: 0.307 AC: 4687 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1407 AN: 5180

South Asian (SAS) AF: 0.249 AC: 1202 AN: 4824

European-Finnish (FIN) AF: 0.0894 AC: 948 AN: 10602

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10845 AN: 67990

Other (OTH) AF: 0.291 AC: 615 AN: 2110

Alfa AF: 0.189 Hom.: 11481

Bravo AF: 0.259

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.33
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs3129299; hg19: chr6-32900787;