chr1-159601379-T-G

Variant names:

• chr1-159601379-T-G
• rs1156060

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.311 AC: 12906 AN: 41436

American (AMR) AF: 0.105 AC: 1602 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3466

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5174

South Asian (SAS) AF: 0.106 AC: 509 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1562 AN: 10596

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8430 AN: 67986

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.0768 Hom.: 114

Bravo AF: 0.171

Asia WGS AF: 0.0870 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.9
DANN	Benign	0.80
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1156060; hg19: chr1-159571169;