rs56037566

Variant names:

• chr16-3064025-T-A
• rs56037566

Your query was ambiguous. Multiple possible variants found:

• chr16-3064025-T-A
• chr16-3064025-T-G

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 0.115 in 152,132 control chromosomes in the GnomAD database, including 1,268 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 0.11 (1268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17458 AN: 152014 Hom.: 1265 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.115 AC: 17494 AN: 152132 Hom.: 1268 Cov.: 32 AF XY: 0.111 AC XY: 8238 AN XY: 74380

African (AFR) AF: 0.184 AC: 7641 AN: 41476

American (AMR) AF: 0.101 AC: 1541 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5178

South Asian (SAS) AF: 0.0689 AC: 332 AN: 4818

European-Finnish (FIN) AF: 0.0396 AC: 420 AN: 10598

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0984 AC: 6690 AN: 68000

Other (OTH) AF: 0.111 AC: 233 AN: 2108

Alfa AF: 0.0366 Hom.: 32

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.82
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs56037566; hg19: chr16-3114026;