rs1552902

Variant names:

• chr1-154636347-C-G
• rs1552902

Your query was ambiguous. Multiple possible variants found:

• chr1-154636347-C-G
• chr1-154636347-C-T

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 0.323 in 151,626 control chromosomes in the GnomAD database, including 7,936 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 0.32 (7936 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.343 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: 0.322 AC: 48856 AN: 151514 Hom.: 7920 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.323 AC: 48908 AN: 151626 Hom.: 7936 Cov.: 31 AF XY: 0.320 AC XY: 23698 AN XY: 74042

African (AFR) AF: 0.292 AC: 12078 AN: 41346

American (AMR) AF: 0.274 AC: 4176 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1213 AN: 3466

East Asian (EAS) AF: 0.310 AC: 1598 AN: 5148

South Asian (SAS) AF: 0.281 AC: 1355 AN: 4816

European-Finnish (FIN) AF: 0.363 AC: 3782 AN: 10412

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23563 AN: 67894

Other (OTH) AF: 0.340 AC: 718 AN: 2112

Alfa AF: 0.197 Hom.: 399

Bravo AF: 0.314

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.35
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs1552902; hg19: chr1-154608823;