rs1257282

Variant names:

• chr14-99362439-G-A
• rs1257282

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.373 AC: 15115 AN: 40494

American (AMR) AF: 0.0574 AC: 872 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3470

East Asian (EAS) AF: 0.0293 AC: 149 AN: 5092

South Asian (SAS) AF: 0.0739 AC: 351 AN: 4750

European-Finnish (FIN) AF: 0.0811 AC: 847 AN: 10448

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0495 AC: 3359 AN: 67800

Other (OTH) AF: 0.103 AC: 215 AN: 2096

Alfa AF: 0.0725 Hom.: 1558

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1257282; hg19: chr14-99828776;