rs605920

Variant names:

• chr18-65217682-C-G
• rs605920

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;