rs1563655

chr16-81442327-G-Achr16-81442327-G-Cchr16-81442327-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 0.436 in 152,000 control chromosomes in the GnomAD database, including 17,006 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 0.44 (17006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 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: 0.435 AC: 66121 AN: 151882 Hom.: 16973 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.436 AC: 66208 AN: 152000 Hom.: 17006 Cov.: 32 AF XY: 0.432 AC XY: 32113 AN XY: 74286

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.401

Alfa AF: 0.334 Hom.: 12390

Bravo AF: 0.454

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.11
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1563655; hg19: chr16-81475932;