rs13375273

Variant names:

• chr1-181849948-G-A
• rs13375273

Your query was ambiguous. Multiple possible variants found:

• chr1-181849948-G-A
• chr1-181849948-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.288 in 152,000 control chromosomes in the GnomAD database, including 6,536 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 (6536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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: 0.288 AC: 43722 AN: 151882 Hom.: 6523 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.288 AC: 43771 AN: 152000 Hom.: 6536 Cov.: 32 AF XY: 0.289 AC XY: 21481 AN XY: 74252

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.286

Alfa AF: 0.290 Hom.: 979

Bravo AF: 0.285

Asia WGS AF: 0.318 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.6
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13375273; hg19: chr1-181819083;