chr5-143270839-T-C

Variant names:

• chr5-143270839-T-C
• rs174048

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;