14-68870428-G-A

Variant names:

• chr14-68870428-G-A
• rs6573861

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 0.69 in 150,222 control chromosomes in the GnomAD database, including 35,958 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 0.69 (35958 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.690 AC: 103616 AN: 150132 Hom.: 35933 Cov.: 27

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.690 AC: 103677 AN: 150222 Hom.: 35958 Cov.: 27 AF XY: 0.691 AC XY: 50606 AN XY: 73256

African (AFR) AF: 0.676 AC: 27552 AN: 40758

American (AMR) AF: 0.770 AC: 11639 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2509 AN: 3466

East Asian (EAS) AF: 0.499 AC: 2564 AN: 5134

South Asian (SAS) AF: 0.749 AC: 3590 AN: 4790

European-Finnish (FIN) AF: 0.662 AC: 6506 AN: 9832

Middle Eastern (MID) AF: 0.672 AC: 195 AN: 290

European-Non Finnish (NFE) AF: 0.693 AC: 47022 AN: 67842

Other (OTH) AF: 0.694 AC: 1452 AN: 2092

Alfa AF: 0.684 Hom.: 4364

Bravo AF: 0.695

Asia WGS AF: 0.702 AC: 2436 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.23
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6573861; hg19: chr14-69337145;