rs2582597

Variant names:

• chr16-60091881-G-A
• rs2582597

Your query was ambiguous. Multiple possible variants found:

• chr16-60091881-G-A
• chr16-60091881-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 0.526 in 151,948 control chromosomes in the GnomAD database, including 21,591 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 0.53 (21591 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 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: 0.526 AC: 79882 AN: 151830 Hom.: 21548 Cov.: 33

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.526 AC: 79985 AN: 151948 Hom.: 21591 Cov.: 33 AF XY: 0.534 AC XY: 39654 AN XY: 74256

African (AFR) AF: 0.594 AC: 24644 AN: 41466

American (AMR) AF: 0.572 AC: 8743 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1483 AN: 3466

East Asian (EAS) AF: 0.802 AC: 4143 AN: 5168

South Asian (SAS) AF: 0.619 AC: 2989 AN: 4826

European-Finnish (FIN) AF: 0.530 AC: 5594 AN: 10546

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30586 AN: 67890

Other (OTH) AF: 0.526 AC: 1107 AN: 2104

Alfa AF: 0.469 Hom.: 68955

Bravo AF: 0.531

Asia WGS AF: 0.700 AC: 2432 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2582597; hg19: chr16-60125785;