ENST00000829864.1:n.273+4867A>T

Variant names:

• chr6-32479076-A-T
• rs17203612
• ENST00000829864.1:n.273+4867A>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+4867A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 134,548 control chromosomes in the GnomAD database, including 11,619 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 0.43 (11619 hom., cov: 31)
• Consequence: ENSG00000307923 ENST00000829864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 12 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829864.1. 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
	ENSG00000307923	ENST00000829864.1		n.273+4867A>T		intron	N/A
	ENSG00000307923	ENST00000829865.1		n.270-60A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 58126 AN: 134442 Hom.: 11612 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.432 AC: 58164 AN: 134548 Hom.: 11619 Cov.: 31 AF XY: 0.431 AC XY: 28409 AN XY: 65912

African (AFR) AF: 0.323 AC: 11436 AN: 35380

American (AMR) AF: 0.482 AC: 6626 AN: 13750

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1659 AN: 3100

East Asian (EAS) AF: 0.413 AC: 1947 AN: 4712

South Asian (SAS) AF: 0.398 AC: 1655 AN: 4162

European-Finnish (FIN) AF: 0.483 AC: 4691 AN: 9716

Middle Eastern (MID) AF: 0.397 AC: 92 AN: 232

European-Non Finnish (NFE) AF: 0.472 AC: 28661 AN: 60766

Other (OTH) AF: 0.442 AC: 822 AN: 1860

Alfa AF: 0.411 Hom.: 925

Asia WGS AF: 0.334 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.77
DANN	Benign	0.22
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17203612; hg19: chr6-32446853;