rs230119

Variant names:

• chr9-119152945-C-A
• rs230119

Your query was ambiguous. Multiple possible variants found:

• chr9-119152945-C-A
• chr9-119152945-C-T

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 0.118 in 152,108 control chromosomes in the GnomAD database, including 2,927 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 0.12 (2927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.118 AC: 17866 AN: 151990 Hom.: 2918 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.118 AC: 17919 AN: 152108 Hom.: 2927 Cov.: 32 AF XY: 0.116 AC XY: 8589 AN XY: 74360

African (AFR) AF: 0.372 AC: 15406 AN: 41434

American (AMR) AF: 0.0676 AC: 1032 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4820

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10604

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0157 AC: 1067 AN: 68006

Other (OTH) AF: 0.102 AC: 216 AN: 2116

Alfa AF: 0.0236 Hom.: 61

Bravo AF: 0.132

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.39
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs230119; hg19: chr9-121915223;