rs1404027

Variant names:

• chr1-105534745-A-G
• rs1404027

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 0.264 in 151,816 control chromosomes in the GnomAD database, including 6,421 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 0.26 (6421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

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 (AFR) allele frequency at 95% confidence interval = 0.444 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: 0.264 AC: 40098 AN: 151702 Hom.: 6406 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.264 AC: 40153 AN: 151816 Hom.: 6421 Cov.: 32 AF XY: 0.260 AC XY: 19319 AN XY: 74168

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.259

Alfa AF: 0.214 Hom.: 1807

Bravo AF: 0.281

Asia WGS AF: 0.219 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404027; hg19: chr1-106077367;