rs7146388

Variant names:

• chr14-43621725-A-G
• rs7146388

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 0.238 in 152,094 control chromosomes in the GnomAD database, including 4,418 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 (4418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 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: 0.238 AC: 36127 AN: 151976 Hom.: 4420 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.238 AC: 36144 AN: 152094 Hom.: 4418 Cov.: 32 AF XY: 0.237 AC XY: 17644 AN XY: 74372

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.223

Alfa AF: 0.254 Hom.: 786

Bravo AF: 0.233

Asia WGS AF: 0.244 AC: 842 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7146388; hg19: chr14-44090928;