9-94131663-A-G

Variant names:

• chr9-94131663-A-G
• rs1257763
• ENST00000654577.1:n.312-12081T>C

Variant summary

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

The ENST00000654577.1(ENSG00000286834):​n.312-12081T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.972 in 152,296 control chromosomes in the GnomAD database, including 71,974 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 0.97 (71974 hom., cov: 32)
• Consequence: ENSG00000286834 ENST00000654577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 37 publications found

Genes affected

ENSG00000286834 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 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
ENSG00000286834	ENST00000654577.1	n.312-12081T>C		intron_variant	Intron 2 of 2
ENSG00000293481	ENST00000715891.1	n.79+822A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.972 AC: 147923 AN: 152178 Hom.: 71913 Cov.: 32

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.972 AC: 148043 AN: 152296 Hom.: 71974 Cov.: 32 AF XY: 0.972 AC XY: 72389 AN XY: 74464

African (AFR) AF: 0.993 AC: 41272 AN: 41550

American (AMR) AF: 0.985 AC: 15075 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3421 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5177 AN: 5180

South Asian (SAS) AF: 0.980 AC: 4731 AN: 4826

European-Finnish (FIN) AF: 0.955 AC: 10131 AN: 10610

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65034 AN: 68028

Other (OTH) AF: 0.972 AC: 2054 AN: 2114

Alfa AF: 0.963 Hom.: 241807

Bravo AF: 0.976

Asia WGS AF: 0.991 AC: 3447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.47
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1257763; hg19: chr9-96893945;