5-142308074-T-C

Position:

• chr5-142308074-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.568 in 151,886 control chromosomes in the GnomAD database, including 24,849 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 0.57 (24849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 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: 0.568 AC: 86150 AN: 151766 Hom.: 24837 Cov.: 31

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.568 AC: 86214 AN: 151886 Hom.: 24849 Cov.: 31 AF XY: 0.564 AC XY: 41891 AN XY: 74224

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.595

Alfa AF: 0.561 Hom.: 6795

Bravo AF: 0.580

Asia WGS AF: 0.430 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6897876; hg19: chr5-141687639;