5-14141728-C-T

Variant names:

• chr5-14141728-C-T
• rs152383

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 0.72 in 152,164 control chromosomes in the GnomAD database, including 40,606 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 0.72 (40606 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.898 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: 0.720 AC: 109501 AN: 152046 Hom.: 40547 Cov.: 33

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.720 AC: 109624 AN: 152164 Hom.: 40606 Cov.: 33 AF XY: 0.713 AC XY: 53024 AN XY: 74384

African (AFR) AF: 0.905 AC: 37611 AN: 41542

American (AMR) AF: 0.675 AC: 10318 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2182 AN: 3468

East Asian (EAS) AF: 0.537 AC: 2780 AN: 5178

South Asian (SAS) AF: 0.729 AC: 3510 AN: 4816

European-Finnish (FIN) AF: 0.569 AC: 6019 AN: 10572

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44897 AN: 67994

Other (OTH) AF: 0.684 AC: 1444 AN: 2112

Alfa AF: 0.684 Hom.: 4253

Bravo AF: 0.731

Asia WGS AF: 0.683 AC: 2373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs152383; hg19: chr5-14141837;