9-118328513-T-C

Variant names:

• chr9-118328513-T-C
• rs1418495

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.519 in 152,044 control chromosomes in the GnomAD database, including 21,441 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 0.52 (21441 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 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: 0.519 AC: 78887 AN: 151926 Hom.: 21431 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.519 AC: 78930 AN: 152044 Hom.: 21441 Cov.: 33 AF XY: 0.519 AC XY: 38567 AN XY: 74306

African (AFR) AF: 0.343 AC: 14210 AN: 41474

American (AMR) AF: 0.589 AC: 8982 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1712 AN: 3466

East Asian (EAS) AF: 0.495 AC: 2560 AN: 5174

South Asian (SAS) AF: 0.500 AC: 2412 AN: 4820

European-Finnish (FIN) AF: 0.603 AC: 6382 AN: 10592

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40854 AN: 67958

Other (OTH) AF: 0.517 AC: 1092 AN: 2114

Alfa AF: 0.572 Hom.: 41984

Bravo AF: 0.514

Asia WGS AF: 0.515 AC: 1792 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.70
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1418495; hg19: chr9-121090791;