chr1-159719598-T-A

Position:

• chr1-159719598-T-A

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 0.324 in 152,092 control chromosomes in the GnomAD database, including 8,586 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 0.32 (8586 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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: 0.324 AC: 49294 AN: 151974 Hom.: 8578 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.324 AC: 49321 AN: 152092 Hom.: 8586 Cov.: 33 AF XY: 0.328 AC XY: 24417 AN XY: 74348

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.343

Alfa AF: 0.332 Hom.: 1126

Bravo AF: 0.321

Asia WGS AF: 0.451 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2027471; hg19: chr1-159689388;