18-60245470-C-T

Variant names:

• chr18-60245470-C-T
• rs9956274

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 0.845 in 152,142 control chromosomes in the GnomAD database, including 56,437 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 0.85 (56437 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.961 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: 0.846 AC: 128559 AN: 152024 Hom.: 56427 Cov.: 31

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.845 AC: 128607 AN: 152142 Hom.: 56437 Cov.: 31 AF XY: 0.852 AC XY: 63359 AN XY: 74380

African (AFR) AF: 0.579 AC: 24012 AN: 41438

American (AMR) AF: 0.899 AC: 13751 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3376 AN: 3472

East Asian (EAS) AF: 0.981 AC: 5063 AN: 5162

South Asian (SAS) AF: 0.984 AC: 4750 AN: 4826

European-Finnish (FIN) AF: 0.982 AC: 10416 AN: 10606

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64230 AN: 68028

Other (OTH) AF: 0.869 AC: 1831 AN: 2108

Alfa AF: 0.915 Hom.: 34827

Bravo AF: 0.825

Asia WGS AF: 0.957 AC: 3328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.060

Splicing

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

Other links and lift over

dbSNP: rs9956274; hg19: chr18-57912703;