rs7150062

Positions:

• chr14-54460932-A-G

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 0.198 in 152,166 control chromosomes in the GnomAD database, including 3,524 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 0.20 (3524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.198 AC: 30083 AN: 152048 Hom.: 3515 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.198 AC: 30147 AN: 152166 Hom.: 3524 Cov.: 32 AF XY: 0.194 AC XY: 14441 AN XY: 74402

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.0893

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.161

Alfa AF: 0.167 Hom.: 1371

Bravo AF: 0.206

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7150062; hg19: chr14-54927650;