rs1257282

chr14-99362439-G-A

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 0.14 in 150,550 control chromosomes in the GnomAD database, including 3,067 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 0.14 (3067 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 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: 0.139 AC: 20927 AN: 150428 Hom.: 3047 Cov.: 30

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.0292

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.140 AC: 21006 AN: 150550 Hom.: 3067 Cov.: 30 AF XY: 0.137 AC XY: 10082 AN XY: 73606

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.0574

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.0293

Gnomad4 SAS AF: 0.0739

Gnomad4 FIN AF: 0.0811

Gnomad4 NFE AF: 0.0495

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0625 Hom.: 826

Bravo AF: 0.149

Asia WGS AF: 0.0950 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.21
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1257282; hg19: chr14-99828776;