9-132370480-A-G

Variant names:

• chr9-132370480-A-G
• rs1185995
• ENST00000792639.1:n.157-4247A>G

Variant summary

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

The ENST00000792639.1(ENSG00000303195):​n.157-4247A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,150 control chromosomes in the GnomAD database, including 60,169 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 (60169 hom., cov: 30)
• Consequence: ENSG00000303195 ENST00000792639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 2 publications found

Genes affected

ENSG00000303195 (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 (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792639.1. 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
	ENSG00000303195	ENST00000792639.1		n.157-4247A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134893 AN: 152032 Hom.: 60139 Cov.: 30

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.887 AC: 134977 AN: 152150 Hom.: 60169 Cov.: 30 AF XY: 0.886 AC XY: 65874 AN XY: 74378

African (AFR) AF: 0.820 AC: 34023 AN: 41484

American (AMR) AF: 0.906 AC: 13837 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3229 AN: 3472

East Asian (EAS) AF: 0.732 AC: 3775 AN: 5160

South Asian (SAS) AF: 0.888 AC: 4275 AN: 4814

European-Finnish (FIN) AF: 0.929 AC: 9856 AN: 10604

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62970 AN: 68022

Other (OTH) AF: 0.899 AC: 1899 AN: 2112

Alfa AF: 0.916 Hom.: 125069

Bravo AF: 0.882

Asia WGS AF: 0.819 AC: 2848 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	0.17
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1185995;

hg19: chr9-135245867;