rs1563655

Variant names:

• chr16-81442327-G-A
• rs1563655

Your query was ambiguous. Multiple possible variants found:

• chr16-81442327-G-A
• chr16-81442327-G-C
• chr16-81442327-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.729 AC: 30192 AN: 41432

American (AMR) AF: 0.375 AC: 5731 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2446 AN: 5174

South Asian (SAS) AF: 0.322 AC: 1551 AN: 4816

European-Finnish (FIN) AF: 0.294 AC: 3106 AN: 10570

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21092 AN: 67944

Other (OTH) AF: 0.401 AC: 846 AN: 2112

Alfa AF: 0.346 Hom.: 17305

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1563655; hg19: chr16-81475932;