14-78046795-A-G

Variant names:

• chr14-78046795-A-G
• rs4020123

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 0.547 in 151,960 control chromosomes in the GnomAD database, including 23,869 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 0.55 (23869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.629 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: 0.548 AC: 83140 AN: 151842 Hom.: 23865 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.547 AC: 83177 AN: 151960 Hom.: 23869 Cov.: 32 AF XY: 0.542 AC XY: 40269 AN XY: 74254

African (AFR) AF: 0.377 AC: 15597 AN: 41426

American (AMR) AF: 0.635 AC: 9691 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3468

East Asian (EAS) AF: 0.505 AC: 2608 AN: 5164

South Asian (SAS) AF: 0.450 AC: 2167 AN: 4816

European-Finnish (FIN) AF: 0.543 AC: 5724 AN: 10534

Middle Eastern (MID) AF: 0.621 AC: 180 AN: 290

European-Non Finnish (NFE) AF: 0.634 AC: 43127 AN: 67972

Other (OTH) AF: 0.618 AC: 1303 AN: 2110

Alfa AF: 0.527 Hom.: 8522

Bravo AF: 0.552

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.25
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4020123; hg19: chr14-78513138;