9-29985817-T-C

Variant names:

• chr9-29985817-T-C
• rs6476179
• ENST00000850881.1:n.227+43397T>C

Variant summary

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

The ENST00000850881.1(ENSG00000310559):​n.227+43397T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,924 control chromosomes in the GnomAD database, including 3,415 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 0.19 (3415 hom., cov: 32)
• Consequence: ENSG00000310559 ENST00000850881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 publications found

Genes affected

ENSG00000310559 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850881.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310559	ENST00000850881.1		n.227+43397T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28569 AN: 151806 Hom.: 3410 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.188 AC: 28599 AN: 151924 Hom.: 3415 Cov.: 32 AF XY: 0.184 AC XY: 13670 AN XY: 74280

African (AFR) AF: 0.331 AC: 13706 AN: 41416

American (AMR) AF: 0.145 AC: 2215 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3464

East Asian (EAS) AF: 0.189 AC: 972 AN: 5152

South Asian (SAS) AF: 0.186 AC: 891 AN: 4802

European-Finnish (FIN) AF: 0.0975 AC: 1032 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8715 AN: 67944

Other (OTH) AF: 0.189 AC: 398 AN: 2108

Alfa AF: 0.151 Hom.: 6777

Bravo AF: 0.195

Asia WGS AF: 0.225 AC: 787 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	2.2
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6476179; hg19: chr9-29985815;