chr18-60175300-G-A

Position:

• chr18-60175300-G-A

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 0.513 in 151,988 control chromosomes in the GnomAD database, including 22,087 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 0.51 (22087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77902 AN: 151870 Hom.: 22046 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.513 AC: 77995 AN: 151988 Hom.: 22087 Cov.: 32 AF XY: 0.508 AC XY: 37720 AN XY: 74268

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.470

Alfa AF: 0.462 Hom.: 7999

Bravo AF: 0.515

Asia WGS AF: 0.393 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1350341; hg19: chr18-57842533;