9-105026971-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000286536 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000299043	ENST00000760085.1	n.235-26264A>G		intron_variant	Intron 1 of 2
ENSG00000299043	ENST00000760086.1	n.215-26264A>G		intron_variant	Intron 1 of 3
ENSG00000299043	ENST00000760087.1	n.190+32921A>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.524 AC: 21678 AN: 41358

American (AMR) AF: 0.577 AC: 8799 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2356 AN: 3470

East Asian (EAS) AF: 0.693 AC: 3558 AN: 5132

South Asian (SAS) AF: 0.566 AC: 2705 AN: 4782

European-Finnish (FIN) AF: 0.575 AC: 6054 AN: 10532

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43772 AN: 67934

Other (OTH) AF: 0.604 AC: 1274 AN: 2108

Alfa AF: 0.635 Hom.: 118301

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs328879; hg19: chr9-107789252;