1-159601379-T-G

Variant names:

• chr1-159601379-T-G
• rs1156060

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 0.17 in 152,074 control chromosomes in the GnomAD database, including 2,850 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 0.17 (2850 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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: 0.169 AC: 25737 AN: 151956 Hom.: 2836 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.170 AC: 25790 AN: 152074 Hom.: 2850 Cov.: 31 AF XY: 0.169 AC XY: 12593 AN XY: 74364

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0799

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0643 Hom.: 72

Bravo AF: 0.171

Asia WGS AF: 0.0870 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1156060; hg19: chr1-159571169;