1-159230230-G-T

Variant names:

• chr1-159230230-G-T
• rs863013

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 0.237 in 152,096 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: 0.184
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 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: 0.237 AC: 36029 AN: 151978 Hom.: 5410 Cov.: 32

Gnomad AFR AF: 0.0599

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.237 AC: 36033 AN: 152096 Hom.: 5407 Cov.: 32 AF XY: 0.236 AC XY: 17530 AN XY: 74338

African (AFR) AF: 0.0598 AC: 2486 AN: 41540

American (AMR) AF: 0.229 AC: 3491 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 758 AN: 3466

East Asian (EAS) AF: 0.199 AC: 1029 AN: 5160

South Asian (SAS) AF: 0.256 AC: 1232 AN: 4816

European-Finnish (FIN) AF: 0.338 AC: 3570 AN: 10552

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22719 AN: 67970

Other (OTH) AF: 0.242 AC: 512 AN: 2112

Alfa AF: 0.287 Hom.: 14182

Bravo AF: 0.219

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.52
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs863013; hg19: chr1-159200020;