chr18-58861664-C-T

Variant names:

• chr18-58861664-C-T
• rs6567030

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 0.431 in 152,056 control chromosomes in the GnomAD database, including 15,873 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 0.43 (15873 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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: 0.431 AC: 65479 AN: 151938 Hom.: 15826 Cov.: 33

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.431 AC: 65584 AN: 152056 Hom.: 15873 Cov.: 33 AF XY: 0.438 AC XY: 32521 AN XY: 74302

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.400

Alfa AF: 0.357 Hom.: 3783

Bravo AF: 0.441

Asia WGS AF: 0.586 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6567030; hg19: chr18-56528896;