rs1112494

chr4-114154887-T-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 0.389 in 152,126 control chromosomes in the GnomAD database, including 12,221 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 0.39 (12221 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 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: 0.389 AC: 59196 AN: 152008 Hom.: 12208 Cov.: 33

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.389 AC: 59228 AN: 152126 Hom.: 12221 Cov.: 33 AF XY: 0.393 AC XY: 29215 AN XY: 74354

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.388

Alfa AF: 0.411 Hom.: 1657

Bravo AF: 0.389

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	7.0
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1112494; hg19: chr4-115076043;