rs1891187

Positions:

• chr1-159659263-T-A

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 0.377 in 152,038 control chromosomes in the GnomAD database, including 11,246 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 0.38 (11246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57300 AN: 151922 Hom.: 11230 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.377 AC: 57358 AN: 152038 Hom.: 11246 Cov.: 32 AF XY: 0.375 AC XY: 27870 AN XY: 74318

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.383

Alfa AF: 0.371 Hom.: 1307

Bravo AF: 0.372

Asia WGS AF: 0.219 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891187; hg19: chr1-159629053;