chr1-55036464-C-G

Variant names:

• chr1-55036464-C-G
• rs2149041

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 0.179 in 152,170 control chromosomes in the GnomAD database, including 3,496 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 0.18 (3496 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 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: 0.179 AC: 27152 AN: 152052 Hom.: 3491 Cov.: 33

Gnomad AFR AF: 0.0768

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.179 AC: 27174 AN: 152170 Hom.: 3496 Cov.: 33 AF XY: 0.180 AC XY: 13387 AN XY: 74382

Gnomad4 AFR AF: 0.0768

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.221

Alfa AF: 0.171 Hom.: 321

Bravo AF: 0.190

Asia WGS AF: 0.400 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2149041; hg19: chr1-55502137;