rs216524

Variant names:

• chr14-60185215-C-A
• rs216524

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 0.475 in 152,088 control chromosomes in the GnomAD database, including 18,005 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 0.48 (18005 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 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: 0.475 AC: 72167 AN: 151970 Hom.: 17983 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.475 AC: 72250 AN: 152088 Hom.: 18005 Cov.: 33 AF XY: 0.469 AC XY: 34866 AN XY: 74350

African (AFR) AF: 0.600 AC: 24882 AN: 41492

American (AMR) AF: 0.472 AC: 7210 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3536 AN: 5184

South Asian (SAS) AF: 0.360 AC: 1737 AN: 4820

European-Finnish (FIN) AF: 0.335 AC: 3540 AN: 10570

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27846 AN: 67956

Other (OTH) AF: 0.484 AC: 1024 AN: 2116

Alfa AF: 0.449 Hom.: 1976

Bravo AF: 0.497

Asia WGS AF: 0.526 AC: 1830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.33
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs216524; hg19: chr14-60651933;