rs1365111

Positions:

• chr3-187675118-G-A

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 0.166 in 152,088 control chromosomes in the GnomAD database, including 2,787 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 0.17 (2787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25265 AN: 151968 Hom.: 2777 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.0781

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.166 AC: 25299 AN: 152088 Hom.: 2787 Cov.: 32 AF XY: 0.165 AC XY: 12274 AN XY: 74354

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.0938

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.0781

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.148

Alfa AF: 0.161 Hom.: 458

Bravo AF: 0.167

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.5
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1365111; hg19: chr3-187392906;