rs188620

Variant names:

• chr14-60222460-A-C
• rs188620

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 0.0877 in 152,240 control chromosomes in the GnomAD database, including 979 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 0.088 (979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 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: 0.0877 AC: 13348 AN: 152122 Hom.: 980 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0606

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0877 AC: 13355 AN: 152240 Hom.: 979 Cov.: 32 AF XY: 0.0855 AC XY: 6369 AN XY: 74472

African (AFR) AF: 0.205 AC: 8500 AN: 41508

American (AMR) AF: 0.0605 AC: 926 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4828

European-Finnish (FIN) AF: 0.0131 AC: 139 AN: 10612

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0465 AC: 3163 AN: 68018

Other (OTH) AF: 0.0933 AC: 197 AN: 2112

Alfa AF: 0.0745 Hom.: 154

Bravo AF: 0.0978

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.66
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs188620; hg19: chr14-60689178;