rs10969197

Variant names:

• chr9-29473784-A-G
• rs10969197
• ENST00000850880.1:n.98+23295A>G

Variant summary

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

The ENST00000850880.1(ENSG00000300941):​n.98+23295A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,242 control chromosomes in the GnomAD database, including 119 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 (119 hom., cov: 33)
• Consequence: ENSG00000300941 ENST00000850880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0768 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
ENSG00000300941	ENST00000850880.1	n.98+23295A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 5197 AN: 152124 Hom.: 116 Cov.: 33

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.0835

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0343

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0342 AC: 5211 AN: 152242 Hom.: 119 Cov.: 33 AF XY: 0.0334 AC XY: 2485 AN XY: 74428

African (AFR) AF: 0.0321 AC: 1335 AN: 41548

American (AMR) AF: 0.0299 AC: 457 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3470

East Asian (EAS) AF: 0.0833 AC: 430 AN: 5164

South Asian (SAS) AF: 0.0269 AC: 130 AN: 4824

European-Finnish (FIN) AF: 0.0218 AC: 231 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0343 AC: 2330 AN: 68012

Other (OTH) AF: 0.0294 AC: 62 AN: 2112

Alfa AF: 0.0341 Hom.: 178

Bravo AF: 0.0369

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.4
DANN	Benign	0.88
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs10969197; hg19: chr9-29473782; COSMIC: COSV69457388;