rs1188445

Variant names:

• chr1-30691029-G-A
• rs1188445

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 0.267 in 151,832 control chromosomes in the GnomAD database, including 7,657 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 0.27 (7657 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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: 0.267 AC: 40456 AN: 151714 Hom.: 7638 Cov.: 30

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.267 AC: 40529 AN: 151832 Hom.: 7657 Cov.: 30 AF XY: 0.265 AC XY: 19688 AN XY: 74190

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.241

Alfa AF: 0.170 Hom.: 2996

Bravo AF: 0.290

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1188445; hg19: chr1-31163876;