9-122586802-T-G

Variant names:

• chr9-122586802-T-G
• rs10818721
• ENST00000431442.3:n.1363-19844T>G

Variant summary

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

The ENST00000431442.3(ENSG00000234156):​n.1363-19844T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,074 control chromosomes in the GnomAD database, including 6,460 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 0.28 (6460 hom., cov: 31)
• Consequence: ENSG00000234156 ENST00000431442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 4 publications found

Genes affected

ENSG00000234156 (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 = 0.579 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
ENSG00000234156	ENST00000431442.3	n.1363-19844T>G		intron_variant	Intron 7 of 9	3
ENSG00000234156	ENST00000723589.1	n.1045-19844T>G		intron_variant	Intron 4 of 4
ENSG00000234156	ENST00000723590.1	n.498-19844T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42048 AN: 151954 Hom.: 6449 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.277 AC: 42095 AN: 152074 Hom.: 6460 Cov.: 31 AF XY: 0.284 AC XY: 21087 AN XY: 74346

African (AFR) AF: 0.220 AC: 9128 AN: 41476

American (AMR) AF: 0.418 AC: 6386 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1136 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3087 AN: 5172

South Asian (SAS) AF: 0.368 AC: 1773 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2478 AN: 10552

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17286 AN: 67988

Other (OTH) AF: 0.296 AC: 625 AN: 2108

Alfa AF: 0.268 Hom.: 14813

Bravo AF: 0.289

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.30
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10818721; hg19: chr9-125349081;