5-142105368-C-T

Variant names:

• chr5-142105368-C-T
• rs735684

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 0.252 in 152,196 control chromosomes in the GnomAD database, including 6,632 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 0.25 (6632 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.251 AC: 38231 AN: 152078 Hom.: 6615 Cov.: 33

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0904

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.252 AC: 38279 AN: 152196 Hom.: 6632 Cov.: 33 AF XY: 0.248 AC XY: 18491 AN XY: 74434

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0906

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.237

Alfa AF: 0.129 Hom.: 310

Bravo AF: 0.260

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735684; hg19: chr5-141484933;