9-105026971-A-G

Variant names:

• chr9-105026971-A-G
• rs328879
• ENST00000666856.1:n.1858-84T>C

Variant summary

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

The ENST00000666856.1(ENSG00000286536):​n.1858-84T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,756 control chromosomes in the GnomAD database, including 27,446 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 0.60 (27446 hom., cov: 30)
• Consequence: ENSG00000286536 ENST00000666856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

Genes affected

ENSG00000286536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286536	ENST00000666856.1	n.1858-84T>C		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90753 AN: 151638 Hom.: 27438 Cov.: 30

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.598 AC: 90801 AN: 151756 Hom.: 27446 Cov.: 30 AF XY: 0.596 AC XY: 44181 AN XY: 74144

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.604

Alfa AF: 0.639 Hom.: 54131

Bravo AF: 0.596

Asia WGS AF: 0.573 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs328879; hg19: chr9-107789252;