rs13375273

chr1-181849948-G-Achr1-181849948-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;