9-841152-C-A

Variant names:

• chr9-841152-C-A
• rs912062
• ENST00000723200.1:n.401+5703G>T

Variant summary

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

The ENST00000723200.1(ENSG00000294371):​n.401+5703G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 151,944 control chromosomes in the GnomAD database, including 60,228 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 0.89 (60228 hom., cov: 29)
• Consequence: ENSG00000294371 ENST00000723200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 9 publications found

Genes affected

ENSG00000294371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723200.1. 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
	ENSG00000294371	ENST00000723200.1		n.401+5703G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.888 AC: 134859 AN: 151826 Hom.: 60188 Cov.: 29

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.888 AC: 134957 AN: 151944 Hom.: 60228 Cov.: 29 AF XY: 0.887 AC XY: 65830 AN XY: 74256

African (AFR) AF: 0.811 AC: 33591 AN: 41428

American (AMR) AF: 0.845 AC: 12906 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3336 AN: 3472

East Asian (EAS) AF: 0.795 AC: 4059 AN: 5106

South Asian (SAS) AF: 0.879 AC: 4203 AN: 4784

European-Finnish (FIN) AF: 0.951 AC: 10059 AN: 10582

Middle Eastern (MID) AF: 0.925 AC: 270 AN: 292

European-Non Finnish (NFE) AF: 0.937 AC: 63732 AN: 67988

Other (OTH) AF: 0.895 AC: 1890 AN: 2112

Alfa AF: 0.918 Hom.: 193365

Bravo AF: 0.877

Asia WGS AF: 0.830 AC: 2887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.31
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs912062; hg19: chr9-841152;