rs10969194

Variant names:

• chr9-29472998-G-A
• rs10969194
• ENST00000850880.1:n.98+22509G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-29472998-G-A
• chr9-29472998-G-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+22509G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 152,218 control chromosomes in the GnomAD database, including 96 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 0.027 (96 hom., cov: 32)
• Consequence: ENSG00000300941 ENST00000850880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• 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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0762 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+22509G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 4094 AN: 152100 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.00930

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0270 AC: 4108 AN: 152218 Hom.: 96 Cov.: 32 AF XY: 0.0265 AC XY: 1971 AN XY: 74432

African (AFR) AF: 0.00958 AC: 398 AN: 41540

American (AMR) AF: 0.0235 AC: 360 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3468

East Asian (EAS) AF: 0.0827 AC: 426 AN: 5152

South Asian (SAS) AF: 0.0264 AC: 127 AN: 4818

European-Finnish (FIN) AF: 0.0219 AC: 233 AN: 10620

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0340 AC: 2313 AN: 68014

Other (OTH) AF: 0.0227 AC: 48 AN: 2112

Alfa AF: 0.0126 Hom.: 1

Bravo AF: 0.0287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.5
DANN	Benign	0.84
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10969194; hg19: chr9-29472996; COSMIC: COSV69457366;