rs2134456

Variant names:

• chr1-50337914-G-T
• rs2134456

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 0.352 in 151,710 control chromosomes in the GnomAD database, including 10,738 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 0.35 (10738 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.632

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.352 AC: 53368 AN: 151592 Hom.: 10731 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.352 AC: 53385 AN: 151710 Hom.: 10738 Cov.: 32 AF XY: 0.349 AC XY: 25875 AN XY: 74144

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.409

Alfa AF: 0.382 Hom.: 1460

Bravo AF: 0.338

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2134456; hg19: chr1-50803586;