18-60183864-T-C

Variant names:

• chr18-60183864-T-C
• rs17782313

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 0.237 in 152,140 control chromosomes in the GnomAD database, including 4,475 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 0.24 (4475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757
• Publications: 625 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 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: 0.237 AC: 36072 AN: 152022 Hom.: 4474 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.237 AC: 36110 AN: 152140 Hom.: 4475 Cov.: 32 AF XY: 0.234 AC XY: 17380 AN XY: 74402

African (AFR) AF: 0.283 AC: 11745 AN: 41492

American (AMR) AF: 0.158 AC: 2417 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 696 AN: 3472

East Asian (EAS) AF: 0.183 AC: 949 AN: 5178

South Asian (SAS) AF: 0.351 AC: 1689 AN: 4816

European-Finnish (FIN) AF: 0.171 AC: 1809 AN: 10590

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15967 AN: 67990

Other (OTH) AF: 0.223 AC: 471 AN: 2110

Alfa AF: 0.234 Hom.: 17366

Bravo AF: 0.236

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.73
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs17782313; hg19: chr18-57851097;