1-152578800-A-G

Variant names:

• chr1-152578800-A-G
• rs4112788

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 0.669 in 151,748 control chromosomes in the GnomAD database, including 34,233 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 0.67 (34233 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.05
• Publications: 72 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101476 AN: 151630 Hom.: 34189 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.669 AC: 101567 AN: 151748 Hom.: 34233 Cov.: 31 AF XY: 0.671 AC XY: 49700 AN XY: 74106

African (AFR) AF: 0.737 AC: 30533 AN: 41434

American (AMR) AF: 0.641 AC: 9644 AN: 15054

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3161 AN: 5146

South Asian (SAS) AF: 0.634 AC: 3056 AN: 4820

European-Finnish (FIN) AF: 0.665 AC: 7014 AN: 10542

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43950 AN: 67972

Other (OTH) AF: 0.635 AC: 1335 AN: 2102

Alfa AF: 0.649 Hom.: 74918

Bravo AF: 0.667

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.43
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4112788; hg19: chr1-152551276;