rs1877455

Variant names:

• chr1-114556471-C-T
• rs1877455

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 0.125 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
• Publications: 8 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0877 AC: 3639 AN: 41504

American (AMR) AF: 0.215 AC: 3285 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2145 AN: 5152

South Asian (SAS) AF: 0.377 AC: 1815 AN: 4816

European-Finnish (FIN) AF: 0.187 AC: 1977 AN: 10556

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0779 AC: 5295 AN: 67994

Other (OTH) AF: 0.149 AC: 315 AN: 2112

Alfa AF: 0.108 Hom.: 1036

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
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs1877455; hg19: chr1-115099092;