chr9-29476690-T-C

Variant names:

• chr9-29476690-T-C
• rs10813103
• ENST00000850880.1:n.98+26201T>C

Variant summary

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

The ENST00000850880.1(ENSG00000300941):​n.98+26201T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 152,270 control chromosomes in the GnomAD database, including 99 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 (99 hom., cov: 32)
• Consequence: ENSG00000300941 ENST00000850880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0764 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+26201T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 4106 AN: 152152 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00939

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0830

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0271 AC: 4120 AN: 152270 Hom.: 99 Cov.: 32 AF XY: 0.0266 AC XY: 1977 AN XY: 74462

African (AFR) AF: 0.00967 AC: 402 AN: 41560

American (AMR) AF: 0.0231 AC: 353 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3470

East Asian (EAS) AF: 0.0828 AC: 429 AN: 5180

South Asian (SAS) AF: 0.0267 AC: 129 AN: 4824

European-Finnish (FIN) AF: 0.0221 AC: 235 AN: 10620

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

European-Non Finnish (NFE) AF: 0.0341 AC: 2320 AN: 68012

Other (OTH) AF: 0.0232 AC: 49 AN: 2116

Alfa AF: 0.0291 Hom.: 7

Bravo AF: 0.0284

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs10813103; hg19: chr9-29476688; COSMIC: COSV69457424;