chr1-145711327-T-G

Variant names:

• chr1-145711327-T-G
• rs1471633

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 0.428 in 152,064 control chromosomes in the GnomAD database, including 15,066 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 0.43 (15066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 39 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 = 0.522 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65124 AN: 151946 Hom.: 15065 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.428 AC: 65157 AN: 152064 Hom.: 15066 Cov.: 32 AF XY: 0.427 AC XY: 31745 AN XY: 74310

African (AFR) AF: 0.291 AC: 12084 AN: 41480

American (AMR) AF: 0.418 AC: 6392 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3470

East Asian (EAS) AF: 0.162 AC: 837 AN: 5172

South Asian (SAS) AF: 0.319 AC: 1534 AN: 4812

European-Finnish (FIN) AF: 0.532 AC: 5621 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35794 AN: 67972

Other (OTH) AF: 0.415 AC: 876 AN: 2110

Alfa AF: 0.484 Hom.: 32430

Bravo AF: 0.412

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.59
DANN	Benign	0.65
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1471633; hg19: chr1-145723739;