rs7146149

Variant names:

• chr14-28489017-G-T
• rs7146149

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;