14-77622642-G-A

Variant names:

• chr14-77622642-G-A
• rs4243658

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 0.507 in 152,018 control chromosomes in the GnomAD database, including 20,290 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 0.51 (20290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.599 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: 0.507 AC: 77008 AN: 151900 Hom.: 20258 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.507 AC: 77079 AN: 152018 Hom.: 20290 Cov.: 32 AF XY: 0.505 AC XY: 37542 AN XY: 74310

African (AFR) AF: 0.384 AC: 15901 AN: 41458

American (AMR) AF: 0.609 AC: 9299 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1877 AN: 3464

East Asian (EAS) AF: 0.279 AC: 1440 AN: 5166

South Asian (SAS) AF: 0.570 AC: 2745 AN: 4818

European-Finnish (FIN) AF: 0.512 AC: 5419 AN: 10582

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38541 AN: 67940

Other (OTH) AF: 0.527 AC: 1114 AN: 2114

Alfa AF: 0.544 Hom.: 5824

Bravo AF: 0.507

Asia WGS AF: 0.421 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.63
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4243658; hg19: chr14-78088985;