rs565973

Variant names:

• chr18-65415362-T-G
• rs565973

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 0.506 in 151,462 control chromosomes in the GnomAD database, including 20,478 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 0.51 (20478 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 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: 0.506 AC: 76576 AN: 151342 Hom.: 20452 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.506 AC: 76661 AN: 151462 Hom.: 20478 Cov.: 32 AF XY: 0.500 AC XY: 36999 AN XY: 74018

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.494

Alfa AF: 0.471 Hom.: 22794

Bravo AF: 0.518

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs565973; hg19: chr18-63082598;