chr1-152520083-G-A

Variant names:

• chr1-152520083-G-A
• rs4845783

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 0.792 in 152,116 control chromosomes in the GnomAD database, including 48,172 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 0.79 (48172 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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: 0.791 AC: 120301 AN: 151998 Hom.: 48109 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.792 AC: 120422 AN: 152116 Hom.: 48172 Cov.: 31 AF XY: 0.794 AC XY: 58996 AN XY: 74342

African (AFR) AF: 0.930 AC: 38627 AN: 41532

American (AMR) AF: 0.788 AC: 12040 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2794 AN: 3472

East Asian (EAS) AF: 0.773 AC: 3986 AN: 5156

South Asian (SAS) AF: 0.729 AC: 3505 AN: 4810

European-Finnish (FIN) AF: 0.783 AC: 8287 AN: 10582

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48610 AN: 67968

Other (OTH) AF: 0.789 AC: 1664 AN: 2110

Alfa AF: 0.741 Hom.: 71091

Bravo AF: 0.799

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.18
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4845783; hg19: chr1-152492559;