rs1885567

Variant names:

• chr20-16675319-C-T
• rs1885567

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 0.523 in 152,000 control chromosomes in the GnomAD database, including 20,857 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 0.52 (20857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 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: 0.523 AC: 79495 AN: 151882 Hom.: 20835 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.523 AC: 79558 AN: 152000 Hom.: 20857 Cov.: 32 AF XY: 0.521 AC XY: 38721 AN XY: 74278

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.514

Alfa AF: 0.542 Hom.: 36740

Bravo AF: 0.523

Asia WGS AF: 0.510 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.76
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1885567; hg19: chr20-16655964;