rs1565516

Variant names:

• chr18-66242447-G-A
• rs1565516

Your query was ambiguous. Multiple possible variants found:

• chr18-66242447-G-A
• chr18-66242447-G-C
• chr18-66242447-G-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 0.0915 in 149,780 control chromosomes in the GnomAD database, including 1,573 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 0.091 (1573 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.953

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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: 0.0914 AC: 13682 AN: 149668 Hom.: 1573 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0509

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.00863

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0383

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.0915 AC: 13698 AN: 149780 Hom.: 1573 Cov.: 31 AF XY: 0.0902 AC XY: 6600 AN XY: 73140

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0558

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.00863

Gnomad4 NFE AF: 0.0383

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0219 Hom.: 56

Asia WGS AF: 0.0960 AC: 334 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1565516; hg19: chr18-63909684;