rs1891187

Variant names:

• chr1-159659263-T-A
• rs1891187

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.467 AC: 19382 AN: 41468

American (AMR) AF: 0.288 AC: 4399 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3466

East Asian (EAS) AF: 0.158 AC: 818 AN: 5182

South Asian (SAS) AF: 0.306 AC: 1478 AN: 4824

European-Finnish (FIN) AF: 0.388 AC: 4093 AN: 10556

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24618 AN: 67972

Other (OTH) AF: 0.383 AC: 808 AN: 2108

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
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs1891187; hg19: chr1-159629053;