5-132111411-A-G

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 0.591 in 152,138 control chromosomes in the GnomAD database, including 27,546 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 0.59 (27546 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.668 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: 0.591 AC: 89910 AN: 152020 Hom.: 27531 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.591 AC: 89962 AN: 152138 Hom.: 27546 Cov.: 33 AF XY: 0.592 AC XY: 44043 AN XY: 74364

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.620

Alfa AF: 0.657 Hom.: 75148

Bravo AF: 0.590

Asia WGS AF: 0.524 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.6
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs247008; hg19: chr5-131447104; COSMIC: COSV60199052;