chr1-159659231-A-G

Variant names:

• chr1-159659231-A-G
• rs1891186

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 151,996 control chromosomes in the GnomAD database, including 11,241 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 (11241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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: 57283 AN: 151880 Hom.: 11224 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.377 AC: 57342 AN: 151996 Hom.: 11241 Cov.: 32 AF XY: 0.375 AC XY: 27864 AN XY: 74298

African (AFR) AF: 0.467 AC: 19366 AN: 41444

American (AMR) AF: 0.288 AC: 4403 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1402 AN: 3466

East Asian (EAS) AF: 0.157 AC: 813 AN: 5170

South Asian (SAS) AF: 0.307 AC: 1482 AN: 4824

European-Finnish (FIN) AF: 0.388 AC: 4100 AN: 10560

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24611 AN: 67956

Other (OTH) AF: 0.382 AC: 807 AN: 2110

Alfa AF: 0.362 Hom.: 16921

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	-0.99
CADD	Benign	3.3
DANN	Benign	0.69
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1891186; hg19: chr1-159629021;