18-60202517-C-T

Variant names:

• chr18-60202517-C-T
• rs9947403

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 0.347 in 151,930 control chromosomes in the GnomAD database, including 9,530 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 0.35 (9530 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 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: 0.347 AC: 52689 AN: 151812 Hom.: 9521 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.347 AC: 52723 AN: 151930 Hom.: 9530 Cov.: 31 AF XY: 0.344 AC XY: 25570 AN XY: 74246

African (AFR) AF: 0.422 AC: 17469 AN: 41434

American (AMR) AF: 0.237 AC: 3621 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3468

East Asian (EAS) AF: 0.194 AC: 1000 AN: 5162

South Asian (SAS) AF: 0.440 AC: 2109 AN: 4798

European-Finnish (FIN) AF: 0.327 AC: 3449 AN: 10560

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 22952 AN: 67940

Other (OTH) AF: 0.321 AC: 677 AN: 2112

Alfa AF: 0.338 Hom.: 16285

Bravo AF: 0.341

Asia WGS AF: 0.279 AC: 969 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs9947403; hg19: chr18-57869750; COSMIC: COSV74034506;