6-32433162-G-C

Variant names:

• chr6-32433162-G-C
• rs3129859
• ENST00000766007.1:n.280-2431C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000766007.1(ENSG00000299747):​n.280-2431C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,948 control chromosomes in the GnomAD database, including 6,077 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 0.27 (6077 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 42 publications found

Genes affected

ENSG00000299747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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
ENSG00000299747	ENST00000766007.1	n.280-2431C>G		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1	n.283-930G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41238 AN: 151830 Hom.: 6075 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.272 AC: 41260 AN: 151948 Hom.: 6077 Cov.: 32 AF XY: 0.275 AC XY: 20453 AN XY: 74248

African (AFR) AF: 0.193 AC: 8000 AN: 41428

American (AMR) AF: 0.223 AC: 3399 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3466

East Asian (EAS) AF: 0.189 AC: 981 AN: 5178

South Asian (SAS) AF: 0.275 AC: 1328 AN: 4830

European-Finnish (FIN) AF: 0.447 AC: 4709 AN: 10538

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21316 AN: 67932

Other (OTH) AF: 0.264 AC: 556 AN: 2106

Alfa AF: 0.194 Hom.: 470

Bravo AF: 0.251

Asia WGS AF: 0.247 AC: 860 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
DANN	Benign	0.63
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs3129859; hg19: chr6-32400939;