1-192154581-A-G

Variant names:

• chr1-192154581-A-G
• rs7526348

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 0.449 in 151,938 control chromosomes in the GnomAD database, including 16,248 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 0.45 (16248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 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: 0.449 AC: 68103 AN: 151820 Hom.: 16225 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.449 AC: 68150 AN: 151938 Hom.: 16248 Cov.: 32 AF XY: 0.451 AC XY: 33496 AN XY: 74248

African (AFR) AF: 0.292 AC: 12134 AN: 41484

American (AMR) AF: 0.571 AC: 8718 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3657 AN: 5174

South Asian (SAS) AF: 0.440 AC: 2123 AN: 4824

European-Finnish (FIN) AF: 0.455 AC: 4802 AN: 10554

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33452 AN: 67860

Other (OTH) AF: 0.481 AC: 1014 AN: 2106

Alfa AF: 0.487 Hom.: 21338

Bravo AF: 0.455

Asia WGS AF: 0.512 AC: 1781 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7526348; hg19: chr1-192123711;