9-13564274-T-C

Variant names:

• chr9-13564274-T-C
• rs10491758
• ENST00000664438.1:n.162+10950T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664438.1(ENSG00000226197):​n.162+10950T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,194 control chromosomes in the GnomAD database, including 2,811 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 0.14 (2811 hom., cov: 32)
• Consequence: ENSG00000226197 ENST00000664438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

Genes affected

ENSG00000226197 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.666 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
ENSG00000226197	ENST00000664438.1	n.162+10950T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20609 AN: 152076 Hom.: 2805 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.136 AC: 20640 AN: 152194 Hom.: 2811 Cov.: 32 AF XY: 0.142 AC XY: 10557 AN XY: 74408

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0677

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0712 Hom.: 955

Bravo AF: 0.147

Asia WGS AF: 0.464 AC: 1607 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.9
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491758; hg19: chr9-13564273;