chr3-147816056-C-T

Position:

• chr3-147816056-C-T

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 0.37 in 152,032 control chromosomes in the GnomAD database, including 11,567 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 0.37 (11567 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.370 AC: 56187 AN: 151910 Hom.: 11542 Cov.: 33

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.370 AC: 56262 AN: 152032 Hom.: 11567 Cov.: 33 AF XY: 0.375 AC XY: 27899 AN XY: 74310

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.345

Alfa AF: 0.261 Hom.: 10917

Bravo AF: 0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6785065; hg19: chr3-147533843;