chr5-147106119-T-C

Position:

• chr5-147106119-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 0.42 in 151,950 control chromosomes in the GnomAD database, including 16,466 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 0.42 (16466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.549 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: 0.421 AC: 63869 AN: 151832 Hom.: 16460 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.420 AC: 63883 AN: 151950 Hom.: 16466 Cov.: 32 AF XY: 0.422 AC XY: 31379 AN XY: 74276

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.425

Alfa AF: 0.528 Hom.: 42961

Bravo AF: 0.397

Asia WGS AF: 0.396 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs728937; hg19: chr5-146485682;