chr1-159659231-A-G

Position:

• chr1-159659231-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 0.377 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.382

Alfa AF: 0.361 Hom.: 13401

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891186; hg19: chr1-159629021;