chr18-75731727-A-G

Position:

• chr18-75731727-A-G

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 0.848 in 152,206 control chromosomes in the GnomAD database, including 56,988 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 (56988 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 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: 0.848 AC: 128953 AN: 152090 Hom.: 56982 Cov.: 33

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.848 AC: 128996 AN: 152206 Hom.: 56988 Cov.: 33 AF XY: 0.851 AC XY: 63358 AN XY: 74420

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.958

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.875

Alfa AF: 0.895 Hom.: 9597

Bravo AF: 0.833

Asia WGS AF: 0.912 AC: 3172 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	0.16
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8095315; hg19: chr18-73443682; COSMIC: COSV53434935;