9-95683350-A-G

Position:

• chr9-95683350-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000580326.2(ENSG00000228142):​n.139-1793A>G variant causes a intron, non coding transcript 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: ENST00000580326.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000580326.2	n.139-1793A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000422343.1	n.89-32054A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0121

Gnomad4 AMR AF: 0.0399

Gnomad4 ASJ AF: 0.0550

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00891

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.0734

Gnomad4 OTH AF: 0.0529

Alfa AF: 0.0674 Hom.: 103

Bravo AF: 0.0447

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs817183; hg19: chr9-98445632;