6-32439376-A-T

Variant names:

• chr6-32439376-A-T
• rs3129872
• ENST00000766007.1:n.163-1116T>A

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.163-1116T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,032 control chromosomes in the GnomAD database, including 4,858 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 (4858 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 31 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 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.163-1116T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36177 AN: 151912 Hom.: 4856 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.238 AC: 36200 AN: 152032 Hom.: 4858 Cov.: 31 AF XY: 0.241 AC XY: 17884 AN XY: 74322

African (AFR) AF: 0.145 AC: 6013 AN: 41478

American (AMR) AF: 0.211 AC: 3226 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3468

East Asian (EAS) AF: 0.161 AC: 834 AN: 5184

South Asian (SAS) AF: 0.176 AC: 848 AN: 4820

European-Finnish (FIN) AF: 0.412 AC: 4346 AN: 10542

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19593 AN: 67948

Other (OTH) AF: 0.233 AC: 492 AN: 2108

Alfa AF: 0.271 Hom.: 3279

Bravo AF: 0.220

Asia WGS AF: 0.203 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.62
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs3129872; hg19: chr6-32407153;