chr9-29592838-G-T

Variant names:

• chr9-29592838-G-T
• rs560764
• ENST00000770245.1:n.*224C>A

Variant summary

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

The ENST00000770245.1(ENSG00000300227):​n.*224C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,842 control chromosomes in the GnomAD database, including 16,394 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 0.46 (16394 hom., cov: 32)
• Consequence: ENSG00000300227 ENST00000770245.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 7 publications found

Genes affected

ENSG00000300227 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770245.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300227	ENST00000770245.1		n.*224C>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69324 AN: 151724 Hom.: 16393 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.457 AC: 69344 AN: 151842 Hom.: 16394 Cov.: 32 AF XY: 0.458 AC XY: 33951 AN XY: 74194

African (AFR) AF: 0.338 AC: 14018 AN: 41454

American (AMR) AF: 0.514 AC: 7832 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3462

East Asian (EAS) AF: 0.332 AC: 1709 AN: 5144

South Asian (SAS) AF: 0.351 AC: 1688 AN: 4812

European-Finnish (FIN) AF: 0.539 AC: 5679 AN: 10542

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35269 AN: 67886

Other (OTH) AF: 0.467 AC: 987 AN: 2114

Alfa AF: 0.496 Hom.: 58979

Bravo AF: 0.455

Asia WGS AF: 0.363 AC: 1262 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.40
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs560764; hg19: chr9-29592836; COSMIC: COSV60348908;