9-29438919-A-C

Variant names:

• chr9-29438919-A-C
• rs10969156
• ENST00000775037.1:n.254+11470T>G

Variant summary

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

The ENST00000775037.1(ENSG00000300910):​n.254+11470T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0344 in 152,028 control chromosomes in the GnomAD database, including 121 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 0.034 (121 hom., cov: 32)
• Consequence: ENSG00000300910 ENST00000775037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 0 publications found

Genes affected

ENSG00000300910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0804 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775037.1. 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
	ENSG00000300910	ENST00000775037.1		n.254+11470T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0344 AC: 5227 AN: 151910 Hom.: 118 Cov.: 32

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.0872

Gnomad SAS AF: 0.0266

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0344 AC: 5237 AN: 152028 Hom.: 121 Cov.: 32 AF XY: 0.0337 AC XY: 2503 AN XY: 74274

African (AFR) AF: 0.0328 AC: 1362 AN: 41496

American (AMR) AF: 0.0293 AC: 447 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3470

East Asian (EAS) AF: 0.0871 AC: 445 AN: 5112

South Asian (SAS) AF: 0.0271 AC: 130 AN: 4800

European-Finnish (FIN) AF: 0.0221 AC: 234 AN: 10570

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0342 AC: 2325 AN: 67988

Other (OTH) AF: 0.0298 AC: 63 AN: 2112

Alfa AF: 0.0338 Hom.: 9

Bravo AF: 0.0372

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs10969156; hg19: chr9-29438917; COSMIC: COSV69457094;