chr1-159700546-C-G

Position:

• chr1-159700546-C-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 0.237 in 152,150 control chromosomes in the GnomAD database, including 5,290 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 0.24 (5290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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: 0.237 AC: 36034 AN: 152032 Hom.: 5289 Cov.: 32

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.237 AC: 36051 AN: 152150 Hom.: 5290 Cov.: 32 AF XY: 0.239 AC XY: 17795 AN XY: 74376

Gnomad4 AFR AF: 0.0716

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0611

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.252

Alfa AF: 0.278 Hom.: 819

Bravo AF: 0.229

Asia WGS AF: 0.161 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12755606; hg19: chr1-159670336;