chr1-159689319-C-T

Position:

• chr1-159689319-C-T

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 0.245 in 152,070 control chromosomes in the GnomAD database, including 5,407 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 (5407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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: 0.245 AC: 37223 AN: 151952 Hom.: 5406 Cov.: 32

Gnomad AFR AF: 0.0978

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.245 AC: 37239 AN: 152070 Hom.: 5407 Cov.: 32 AF XY: 0.247 AC XY: 18350 AN XY: 74334

Gnomad4 AFR AF: 0.0975

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0604

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.260

Alfa AF: 0.278 Hom.: 1440

Bravo AF: 0.238

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12749227; hg19: chr1-159659109;