rs6566765

Variant names:

• chr18-73751561-C-T
• rs6566765

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.562 in 152,058 control chromosomes in the GnomAD database, including 25,026 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 0.56 (25026 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.651 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: 0.562 AC: 85440 AN: 151940 Hom.: 25027 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.562 AC: 85449 AN: 152058 Hom.: 25026 Cov.: 33 AF XY: 0.563 AC XY: 41852 AN XY: 74318

African (AFR) AF: 0.381 AC: 15786 AN: 41462

American (AMR) AF: 0.662 AC: 10117 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2089 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2568 AN: 5166

South Asian (SAS) AF: 0.470 AC: 2264 AN: 4820

European-Finnish (FIN) AF: 0.672 AC: 7099 AN: 10566

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43562 AN: 67976

Other (OTH) AF: 0.560 AC: 1182 AN: 2110

Alfa AF: 0.601 Hom.: 53300

Bravo AF: 0.557

Asia WGS AF: 0.448 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs6566765; hg19: chr18-71418796;