9-1325179-A-G

Variant names:

• chr9-1325179-A-G
• rs16927557
• ENST00000822116.1:n.310-1895A>G

Variant summary

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

The ENST00000822116.1(ENSG00000306944):​n.310-1895A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,234 control chromosomes in the GnomAD database, including 3,818 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 0.18 (3818 hom., cov: 33)
• Consequence: ENSG00000306944 ENST00000822116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 3 publications found

Genes affected

ENSG00000306944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822116.1. 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
	ENSG00000306944	ENST00000822116.1		n.310-1895A>G		intron	N/A
	ENSG00000306944	ENST00000822117.1		n.141-1895A>G		intron	N/A
	ENSG00000306944	ENST00000822118.1		n.96-1895A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27716 AN: 152116 Hom.: 3802 Cov.: 33

Gnomad AFR AF: 0.0780

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.182 AC: 27739 AN: 152234 Hom.: 3818 Cov.: 33 AF XY: 0.193 AC XY: 14375 AN XY: 74428

African (AFR) AF: 0.0778 AC: 3234 AN: 41574

American (AMR) AF: 0.332 AC: 5078 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 543 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3441 AN: 5174

South Asian (SAS) AF: 0.167 AC: 806 AN: 4830

European-Finnish (FIN) AF: 0.286 AC: 3023 AN: 10578

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11173 AN: 68004

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.178 Hom.: 7073

Bravo AF: 0.187

Asia WGS AF: 0.396 AC: 1372 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.69
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs16927557; hg19: chr9-1325179;