rs216518

Variant names:

• chr14-60216712-C-A
• rs216518

Your query was ambiguous. Multiple possible variants found:

• chr14-60216712-C-A
• chr14-60216712-C-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 0.152 in 152,218 control chromosomes in the GnomAD database, including 1,834 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 0.15 (1834 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23111 AN: 152100 Hom.: 1841 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.152 AC: 23098 AN: 152218 Hom.: 1834 Cov.: 33 AF XY: 0.155 AC XY: 11565 AN XY: 74414

African (AFR) AF: 0.174 AC: 7219 AN: 41516

American (AMR) AF: 0.123 AC: 1877 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3470

East Asian (EAS) AF: 0.0591 AC: 307 AN: 5192

South Asian (SAS) AF: 0.315 AC: 1521 AN: 4826

European-Finnish (FIN) AF: 0.145 AC: 1537 AN: 10586

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9475 AN: 68008

Other (OTH) AF: 0.165 AC: 349 AN: 2116

Alfa AF: 0.142 Hom.: 7616

Bravo AF: 0.146

Asia WGS AF: 0.167 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	2.1
DANN	Benign	0.79
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs216518; hg19: chr14-60683430;