chr9-25416558-T-G

Variant names:

• chr9-25416558-T-G
• rs1831078
• ENST00000732866.1:n.503+2782A>C

Variant summary

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

The ENST00000732866.1(ENSG00000295812):​n.503+2782A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,584 control chromosomes in the GnomAD database, including 36,972 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 0.69 (36972 hom., cov: 31)
• Consequence: ENSG00000295812 ENST00000732866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 2 publications found

Genes affected

ENSG00000295812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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
ENSG00000295812	ENST00000732866.1	n.503+2782A>C		intron_variant	Intron 4 of 4
ENSG00000295812	ENST00000732867.1	n.492+2782A>C		intron_variant	Intron 4 of 4
ENSG00000295812	ENST00000732868.1	n.403+2782A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.693 AC: 104937 AN: 151468 Hom.: 36948 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.693 AC: 105008 AN: 151584 Hom.: 36972 Cov.: 31 AF XY: 0.699 AC XY: 51758 AN XY: 74048

African (AFR) AF: 0.573 AC: 23671 AN: 41344

American (AMR) AF: 0.714 AC: 10858 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2686 AN: 3466

East Asian (EAS) AF: 0.952 AC: 4899 AN: 5146

South Asian (SAS) AF: 0.805 AC: 3879 AN: 4816

European-Finnish (FIN) AF: 0.765 AC: 8042 AN: 10506

Middle Eastern (MID) AF: 0.731 AC: 212 AN: 290

European-Non Finnish (NFE) AF: 0.715 AC: 48485 AN: 67796

Other (OTH) AF: 0.716 AC: 1509 AN: 2108

Alfa AF: 0.711 Hom.: 64270

Bravo AF: 0.685

Asia WGS AF: 0.884 AC: 3074 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.058
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1831078; hg19: chr9-25416556;