1-52370467-G-A

Variant names:

• chr1-52370467-G-A
• rs9633423

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 0.291 in 152,006 control chromosomes in the GnomAD database, including 8,281 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 0.29 (8281 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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: 0.291 AC: 44275 AN: 151888 Hom.: 8283 Cov.: 32

Gnomad AFR AF: 0.0711

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.291 AC: 44278 AN: 152006 Hom.: 8281 Cov.: 32 AF XY: 0.301 AC XY: 22384 AN XY: 74296

African (AFR) AF: 0.0709 AC: 2939 AN: 41462

American (AMR) AF: 0.461 AC: 7049 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3203 AN: 5176

South Asian (SAS) AF: 0.297 AC: 1434 AN: 4828

European-Finnish (FIN) AF: 0.436 AC: 4588 AN: 10534

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 22968 AN: 67950

Other (OTH) AF: 0.311 AC: 657 AN: 2110

Alfa AF: 0.320 Hom.: 26085

Bravo AF: 0.287

Asia WGS AF: 0.388 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9633423; hg19: chr1-52836139; COSMIC: COSV52559429;