rs605920

chr18-65217682-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.647 in 152,022 control chromosomes in the GnomAD database, including 32,677 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 0.65 (32677 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 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: 0.647 AC: 98259 AN: 151904 Hom.: 32626 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.647 AC: 98365 AN: 152022 Hom.: 32677 Cov.: 31 AF XY: 0.646 AC XY: 48006 AN XY: 74336

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.658

Alfa AF: 0.616 Hom.: 3629

Bravo AF: 0.660

Asia WGS AF: 0.624 AC: 2165 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
Cadd	Benign	19
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs605920; hg19: chr18-62884918;