6-32447303-G-A

Variant names:

• chr6-32447303-G-A
• rs3129891
• ENST00000766007.1:n.163-9043C>T

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.163-9043C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,040 control chromosomes in the GnomAD database, including 3,226 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 0.20 (3226 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 30 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766007.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000299747	ENST00000766007.1		n.163-9043C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31030 AN: 151922 Hom.: 3228 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.204 AC: 31042 AN: 152040 Hom.: 3226 Cov.: 31 AF XY: 0.202 AC XY: 15046 AN XY: 74310

African (AFR) AF: 0.197 AC: 8174 AN: 41460

American (AMR) AF: 0.163 AC: 2487 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1458 AN: 5174

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4830

European-Finnish (FIN) AF: 0.219 AC: 2307 AN: 10552

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14267 AN: 67968

Other (OTH) AF: 0.207 AC: 437 AN: 2110

Alfa AF: 0.216 Hom.: 10819

Bravo AF: 0.197

Asia WGS AF: 0.272 AC: 943 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	0.59
DANN	Benign	0.29
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs3129891; hg19: chr6-32415080;