5-143270839-T-C

Position:

• chr5-143270839-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.138 in 152,250 control chromosomes in the GnomAD database, including 1,604 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 0.14 (1604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20989 AN: 152132 Hom.: 1599 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.0784

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.0708

Gnomad SAS AF: 0.0331

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.138 AC: 21028 AN: 152250 Hom.: 1604 Cov.: 32 AF XY: 0.137 AC XY: 10192 AN XY: 74438

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0783

Gnomad4 ASJ AF: 0.0623

Gnomad4 EAS AF: 0.0707

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.114

Alfa AF: 0.144 Hom.: 1196

Bravo AF: 0.129

Asia WGS AF: 0.0690 AC: 241 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	6.0
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs174048; hg19: chr5-142650404;