rs1175381

chr3-12444345-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0263 in 152,264 control chromosomes in the GnomAD database, including 64 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 0.026 (64 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0263 (4003/152264) while in subpopulation NFE AF= 0.0389 (2644/68010). AF 95% confidence interval is 0.0376. There are 64 homozygotes in gnomad4. There are 1953 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 64 gene

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: 0.0263 AC: 4001 AN: 152146 Hom.: 64 Cov.: 32

Gnomad AFR AF: 0.00625

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00476

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0263 AC: 4003 AN: 152264 Hom.: 64 Cov.: 32 AF XY: 0.0262 AC XY: 1953 AN XY: 74450

Gnomad4 AFR AF: 0.00623

Gnomad4 AMR AF: 0.0284

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00476

Gnomad4 FIN AF: 0.0406

Gnomad4 NFE AF: 0.0389

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0365 Hom.: 90

Bravo AF: 0.0244

Asia WGS AF: 0.00491 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1175381; hg19: chr3-12485844;