rs1933752

Variant names:

• chr6-144864133-T-C
• rs1933752

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 0.348 in 152,116 control chromosomes in the GnomAD database, including 10,299 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 0.35 (10299 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.348 AC: 52868 AN: 151998 Hom.: 10271 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.348 AC: 52942 AN: 152116 Hom.: 10299 Cov.: 33 AF XY: 0.354 AC XY: 26288 AN XY: 74346

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.365

Alfa AF: 0.278 Hom.: 2892

Bravo AF: 0.372

Asia WGS AF: 0.568 AC: 1975 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	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1933752; hg19: chr6-145185269;