6-32482312-G-T

Variant names:

• chr6-32482312-G-T
• rs5020946
• ENST00000829864.1:n.273+8103G>T

Variant summary

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

The ENST00000829864.1(ENSG00000307923):​n.273+8103G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 149,662 control chromosomes in the GnomAD database, including 10,792 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 0.37 (10792 hom., cov: 35)
• Consequence: ENSG00000307923 ENST00000829864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 35 publications found

Genes affected

ENSG00000307923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 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
ENSG00000307923	ENST00000829864.1	n.273+8103G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 55540 AN: 149548 Hom.: 10788 Cov.: 35

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.371 AC: 55574 AN: 149662 Hom.: 10792 Cov.: 35 AF XY: 0.370 AC XY: 27076 AN XY: 73100

African (AFR) AF: 0.263 AC: 10760 AN: 40870

American (AMR) AF: 0.420 AC: 6291 AN: 14982

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1568 AN: 3390

East Asian (EAS) AF: 0.364 AC: 1848 AN: 5076

South Asian (SAS) AF: 0.315 AC: 1474 AN: 4680

European-Finnish (FIN) AF: 0.434 AC: 4505 AN: 10386

Middle Eastern (MID) AF: 0.285 AC: 81 AN: 284

European-Non Finnish (NFE) AF: 0.413 AC: 27713 AN: 67022

Other (OTH) AF: 0.372 AC: 776 AN: 2086

Alfa AF: 0.408 Hom.: 8154

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.29
DANN	Benign	0.28
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs5020946; hg19: chr6-32450089;