18-77168012-G-A

Position:

• chr18-77168012-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 0.118 in 152,188 control chromosomes in the GnomAD database, including 1,101 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 0.12 (1101 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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: 0.117 AC: 17865 AN: 152070 Hom.: 1087 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.0822

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.118 AC: 17928 AN: 152188 Hom.: 1101 Cov.: 33 AF XY: 0.118 AC XY: 8761 AN XY: 74402

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.0826

Gnomad4 SAS AF: 0.0873

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.126

Alfa AF: 0.105 Hom.: 397

Bravo AF: 0.117

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1789139; hg19: chr18-74879968;