rs605920

Variant names:

• chr18-65217682-C-G
• rs605920

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.800 AC: 33200 AN: 41494

American (AMR) AF: 0.631 AC: 9630 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2238 AN: 3470

East Asian (EAS) AF: 0.504 AC: 2594 AN: 5144

South Asian (SAS) AF: 0.674 AC: 3245 AN: 4812

European-Finnish (FIN) AF: 0.515 AC: 5444 AN: 10564

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39908 AN: 67962

Other (OTH) AF: 0.658 AC: 1389 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	19
DANN	Benign	0.66
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs605920; hg19: chr18-62884918;