chr9-114842790-T-C

Variant names:

• chr9-114842790-T-C
• rs11554257

Variant summary

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

The variant allele was found at a frequency of 0.136 in 151,600 control chromosomes in the GnomAD database, including 1,464 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 (1464 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 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

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20631 AN: 151482 Hom.: 1466 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.136 AC: 20651 AN: 151600 Hom.: 1464 Cov.: 31 AF XY: 0.137 AC XY: 10165 AN XY: 74038

African (AFR) AF: 0.127 AC: 5242 AN: 41322

American (AMR) AF: 0.176 AC: 2682 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 317 AN: 3462

East Asian (EAS) AF: 0.200 AC: 1028 AN: 5152

South Asian (SAS) AF: 0.211 AC: 1007 AN: 4780

European-Finnish (FIN) AF: 0.0869 AC: 910 AN: 10474

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.132 AC: 8962 AN: 67900

Other (OTH) AF: 0.136 AC: 285 AN: 2100

Alfa AF: 0.133 Hom.: 5402

Bravo AF: 0.139

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11554257; hg19: chr9-117605070;