18-60921894-T-C

Position:

• chr18-60921894-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.562 in 151,800 control chromosomes in the GnomAD database, including 24,649 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 0.56 (24649 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85174 AN: 151680 Hom.: 24601 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.562 AC: 85270 AN: 151800 Hom.: 24649 Cov.: 31 AF XY: 0.561 AC XY: 41596 AN XY: 74204

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.498

Alfa AF: 0.510 Hom.: 23006

Bravo AF: 0.567

Asia WGS AF: 0.415 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1497965; hg19: chr18-58589127;