1-154890719-A-G

Variant names:

• chr1-154890719-A-G
• rs4845680

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 0.53 in 152,106 control chromosomes in the GnomAD database, including 22,779 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 0.53 (22779 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.530 AC: 80601 AN: 151988 Hom.: 22741 Cov.: 33

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.530 AC: 80688 AN: 152106 Hom.: 22779 Cov.: 33 AF XY: 0.536 AC XY: 39856 AN XY: 74356

African (AFR) AF: 0.660 AC: 27379 AN: 41476

American (AMR) AF: 0.591 AC: 9039 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4562 AN: 5186

South Asian (SAS) AF: 0.626 AC: 3016 AN: 4820

European-Finnish (FIN) AF: 0.420 AC: 4439 AN: 10572

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28920 AN: 67978

Other (OTH) AF: 0.517 AC: 1091 AN: 2112

Alfa AF: 0.447 Hom.: 6888

Bravo AF: 0.549

Asia WGS AF: 0.746 AC: 2588 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4845680; hg19: chr1-154863195;