rs7146149

chr14-28489017-G-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 0.24 in 152,104 control chromosomes in the GnomAD database, including 4,646 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 0.24 (4646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36529 AN: 151986 Hom.: 4642 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.240 AC: 36536 AN: 152104 Hom.: 4646 Cov.: 32 AF XY: 0.239 AC XY: 17798 AN XY: 74350

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.271

Alfa AF: 0.275 Hom.: 1179

Bravo AF: 0.236

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.1
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7146149; hg19: chr14-28958223;