6-32474484-T-C

Variant names:

• chr6-32474484-T-C
• rs6901541
• ENST00000829864.1:n.273+275T>C

Variant summary

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

The ENST00000829864.1(ENSG00000307923):​n.273+275T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 114,408 control chromosomes in the GnomAD database, including 3,766 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 0.29 (3766 hom., cov: 29)
• Consequence: ENSG00000307923 ENST00000829864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 22 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307923	ENST00000829864.1		n.273+275T>C		intron	N/A
	ENSG00000307923	ENST00000829865.1		n.269+275T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.295 AC: 33693 AN: 114312 Hom.: 3766 Cov.: 29

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.295 AC: 33714 AN: 114408 Hom.: 3766 Cov.: 29 AF XY: 0.295 AC XY: 16523 AN XY: 55934

African (AFR) AF: 0.306 AC: 9707 AN: 31688

American (AMR) AF: 0.310 AC: 3462 AN: 11150

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 653 AN: 2452

East Asian (EAS) AF: 0.175 AC: 663 AN: 3778

South Asian (SAS) AF: 0.245 AC: 835 AN: 3410

European-Finnish (FIN) AF: 0.381 AC: 3301 AN: 8656

Middle Eastern (MID) AF: 0.241 AC: 54 AN: 224

European-Non Finnish (NFE) AF: 0.285 AC: 14503 AN: 50886

Other (OTH) AF: 0.292 AC: 460 AN: 1574

Alfa AF: 0.298 Hom.: 5366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.1
DANN	Benign	0.50
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6901541; hg19: chr6-32442261;