chr9-29469229-C-T

Variant names:

• chr9-29469229-C-T
• rs10969189
• ENST00000850880.1:n.98+18740C>T

Variant summary

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

The ENST00000850880.1(ENSG00000300941):​n.98+18740C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 143,390 control chromosomes in the GnomAD database, including 97 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 0.028 (97 hom., cov: 30)
• Consequence: ENSG00000300941 ENST00000850880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 0 publications found

Genes affected

ENSG00000300941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0769 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850880.1. 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
	ENSG00000300941	ENST00000850880.1		n.98+18740C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0279 AC: 3996 AN: 143356 Hom.: 94 Cov.: 30

Gnomad AFR AF: 0.00940

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.0163

Gnomad EAS AF: 0.0838

Gnomad SAS AF: 0.0273

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.0408

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0232

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

GnomAD4 genome AF: 0.0280 AC: 4011 AN: 143390 Hom.: 97 Cov.: 30 AF XY: 0.0275 AC XY: 1907 AN XY: 69310

African (AFR) AF: 0.00972 AC: 375 AN: 38576

American (AMR) AF: 0.0246 AC: 351 AN: 14280

Ashkenazi Jewish (ASJ) AF: 0.0163 AC: 56 AN: 3432

East Asian (EAS) AF: 0.0836 AC: 409 AN: 4894

South Asian (SAS) AF: 0.0281 AC: 126 AN: 4478

European-Finnish (FIN) AF: 0.0252 AC: 204 AN: 8104

Middle Eastern (MID) AF: 0.0448 AC: 12 AN: 268

European-Non Finnish (NFE) AF: 0.0346 AC: 2299 AN: 66462

Other (OTH) AF: 0.0230 AC: 46 AN: 1998

Alfa AF: 0.0123 Hom.: 1

Bravo AF: 0.0285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.61
DANN	Benign	0.52
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs10969189; hg19: chr9-29469227; COSMIC: COSV69457338;