rs1122359

chr14-95959443-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 0.123 in 151,992 control chromosomes in the GnomAD database, including 1,430 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 0.12 (1430 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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 (EAS) allele frequency at 95% confidence interval = 0.201 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: 0.123 AC: 18697 AN: 151874 Hom.: 1430 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.123 AC: 18698 AN: 151992 Hom.: 1430 Cov.: 32 AF XY: 0.125 AC XY: 9265 AN XY: 74290

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.139

Alfa AF: 0.154 Hom.: 1536

Bravo AF: 0.121

Asia WGS AF: 0.167 AC: 579 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	1.6
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1122359; hg19: chr14-96425780;