rs1404027

Positions:

• chr1-105534745-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;