rs1877455

chr1-114556471-C-T

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 0.125 in 152,066 control chromosomes in the GnomAD database, including 1,837 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 0.12 (1837 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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: 0.125 AC: 18966 AN: 151948 Hom.: 1830 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.125 AC: 19001 AN: 152066 Hom.: 1837 Cov.: 32 AF XY: 0.137 AC XY: 10148 AN XY: 74338

Gnomad4 AFR AF: 0.0877

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.0779

Gnomad4 OTH AF: 0.149

Alfa AF: 0.104 Hom.: 653

Bravo AF: 0.125

Asia WGS AF: 0.381 AC: 1320 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.1
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1877455; hg19: chr1-115099092;