rs6566765

Positions:

• chr18-73751561-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 0.562 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.560

Alfa AF: 0.600 Hom.: 7583

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6566765; hg19: chr18-71418796;