ENST00000822116.1:n.573-890G>A

Variant names:

• chr9-1332257-G-A
• rs999924
• ENST00000822116.1:n.573-890G>A

Variant summary

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

The ENST00000822116.1(ENSG00000306944):​n.573-890G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,972 control chromosomes in the GnomAD database, including 10,491 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 0.36 (10491 hom., cov: 32)
• Consequence: ENSG00000306944 ENST00000822116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 4 publications found

Genes affected

ENSG00000306944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822116.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306944	ENST00000822116.1		n.573-890G>A		intron	N/A
	ENSG00000306944	ENST00000822117.1		n.404-890G>A		intron	N/A
	ENSG00000306944	ENST00000822118.1		n.359-890G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54256 AN: 151854 Hom.: 10469 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.357 AC: 54308 AN: 151972 Hom.: 10491 Cov.: 32 AF XY: 0.369 AC XY: 27379 AN XY: 74298

African (AFR) AF: 0.393 AC: 16289 AN: 41430

American (AMR) AF: 0.441 AC: 6730 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3383 AN: 5178

South Asian (SAS) AF: 0.383 AC: 1845 AN: 4822

European-Finnish (FIN) AF: 0.445 AC: 4693 AN: 10542

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

European-Non Finnish (NFE) AF: 0.281 AC: 19093 AN: 67948

Other (OTH) AF: 0.336 AC: 707 AN: 2106

Alfa AF: 0.298 Hom.: 9620

Bravo AF: 0.359

Asia WGS AF: 0.528 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.78
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs999924; hg19: chr9-1332257;