5-143438741-T-C

Variant names:

• chr5-143438741-T-C
• rs4912913

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 0.477 in 152,010 control chromosomes in the GnomAD database, including 17,573 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 0.48 (17573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• Publications: 13 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 (NFE) allele frequency at 95% confidence interval = 0.527 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: 0.477 AC: 72394 AN: 151892 Hom.: 17564 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.477 AC: 72449 AN: 152010 Hom.: 17573 Cov.: 32 AF XY: 0.471 AC XY: 35012 AN XY: 74304

African (AFR) AF: 0.444 AC: 18380 AN: 41438

American (AMR) AF: 0.397 AC: 6057 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1673 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1651 AN: 5178

South Asian (SAS) AF: 0.358 AC: 1726 AN: 4824

European-Finnish (FIN) AF: 0.498 AC: 5258 AN: 10568

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.531 AC: 36112 AN: 67950

Other (OTH) AF: 0.489 AC: 1032 AN: 2112

Alfa AF: 0.512 Hom.: 21217

Bravo AF: 0.467

Asia WGS AF: 0.393 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.38
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs4912913; hg19: chr5-142818306;