chr9-95683350-A-G

Variant names:

• chr9-95683350-A-G
• rs817183
• ENST00000422343.2:n.149-32054A>G

Variant summary

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

The ENST00000580326.3(ENSG00000228142):​n.144-1793A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0528 in 152,210 control chromosomes in the GnomAD database, including 333 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 0.053 (333 hom., cov: 30)
• Consequence: ENSG00000228142 ENST00000580326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 2 publications found

Genes affected

ENSG00000228142 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580326.3. 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
	ENSG00000228142	ENST00000422343.2	TSL:5	n.149-32054A>G		intron	N/A
	ENSG00000228142	ENST00000580326.3	TSL:3	n.144-1793A>G		intron	N/A
	ENSG00000228142	ENST00000821223.1		n.143+33109A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0529 AC: 8043 AN: 152092 Hom.: 333 Cov.: 30

Gnomad AFR AF: 0.0122

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00890

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0528 AC: 8043 AN: 152210 Hom.: 333 Cov.: 30 AF XY: 0.0531 AC XY: 3949 AN XY: 74402

African (AFR) AF: 0.0121 AC: 504 AN: 41540

American (AMR) AF: 0.0399 AC: 610 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.00891 AC: 43 AN: 4828

European-Finnish (FIN) AF: 0.141 AC: 1489 AN: 10572

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4989 AN: 68008

Other (OTH) AF: 0.0529 AC: 112 AN: 2116

Alfa AF: 0.0680 Hom.: 167

Bravo AF: 0.0447

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.67
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs817183; hg19: chr9-98445632;