9-89949507-A-G

Variant names:

• chr9-89949507-A-G
• rs2196923
• ENST00000656288.1:n.229-28769A>G

Variant summary

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

The ENST00000656288.1(ENSG00000237626):​n.229-28769A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,054 control chromosomes in the GnomAD database, including 9,561 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 0.31 (9561 hom., cov: 32)
• Consequence: ENSG00000237626 ENST00000656288.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 publications found

Genes affected

ENSG00000237626 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 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
ENSG00000237626	ENST00000656288.1	n.229-28769A>G		intron_variant	Intron 2 of 6
ENSG00000237626	ENST00000659397.1	n.163-28769A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.309 AC: 47000 AN: 151936 Hom.: 9546 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.310 AC: 47062 AN: 152054 Hom.: 9561 Cov.: 32 AF XY: 0.308 AC XY: 22877 AN XY: 74334

African (AFR) AF: 0.577 AC: 23908 AN: 41452

American (AMR) AF: 0.240 AC: 3661 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1842 AN: 5158

South Asian (SAS) AF: 0.0951 AC: 458 AN: 4818

European-Finnish (FIN) AF: 0.189 AC: 2004 AN: 10578

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13222 AN: 67986

Other (OTH) AF: 0.286 AC: 605 AN: 2112

Alfa AF: 0.238 Hom.: 16577

Bravo AF: 0.331

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.042
DANN	Benign	0.49
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2196923; hg19: chr9-92711789;