rs6567030

Positions:

• chr18-58861664-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;