5-132111411-A-G

Variant names:

• chr5-132111411-A-G
• rs247008

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;