9-108032463-G-A

Variant names:

• chr9-108032463-G-A
• rs7850481
• ENST00000798334.1:n.101+20738C>T

Variant summary

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

The ENST00000798334.1(ENSG00000303954):​n.101+20738C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,918 control chromosomes in the GnomAD database, including 13,399 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 0.40 (13399 hom., cov: 32)
• Consequence: ENSG00000303954 ENST00000798334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 1 publications found

Genes affected

ENSG00000303954 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798334.1. 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
	ENSG00000303954	ENST00000798334.1		n.101+20738C>T		intron	N/A
	ENSG00000303954	ENST00000798335.1		n.102-15438C>T		intron	N/A
	ENSG00000303954	ENST00000798336.1		n.102-15438C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60812 AN: 151800 Hom.: 13387 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.401 AC: 60855 AN: 151918 Hom.: 13399 Cov.: 32 AF XY: 0.413 AC XY: 30636 AN XY: 74244

African (AFR) AF: 0.256 AC: 10606 AN: 41432

American (AMR) AF: 0.582 AC: 8880 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3470

East Asian (EAS) AF: 0.617 AC: 3174 AN: 5142

South Asian (SAS) AF: 0.677 AC: 3255 AN: 4806

European-Finnish (FIN) AF: 0.471 AC: 4970 AN: 10544

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27208 AN: 67938

Other (OTH) AF: 0.430 AC: 908 AN: 2112

Alfa AF: 0.384 Hom.: 1419

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.0
DANN	Benign	0.96
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7850481; hg19: chr9-110794744;