chr1-153363542-C-G

Variant names:

• chr1-153363542-C-G
• rs724781

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 0.226 in 152,134 control chromosomes in the GnomAD database, including 4,755 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 0.23 (4755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 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: 0.226 AC: 34359 AN: 152016 Hom.: 4747 Cov.: 32

Gnomad AFR AF: 0.0643

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.226 AC: 34369 AN: 152134 Hom.: 4755 Cov.: 32 AF XY: 0.227 AC XY: 16899 AN XY: 74350

African (AFR) AF: 0.0641 AC: 2665 AN: 41556

American (AMR) AF: 0.328 AC: 5014 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3472

East Asian (EAS) AF: 0.373 AC: 1924 AN: 5156

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4818

European-Finnish (FIN) AF: 0.289 AC: 3050 AN: 10556

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18893 AN: 67984

Other (OTH) AF: 0.272 AC: 573 AN: 2110

Alfa AF: 0.243 Hom.: 646

Bravo AF: 0.226

Asia WGS AF: 0.309 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs724781; hg19: chr1-153336018;