chr5-132111411-A-G

Variant names:

• chr5-132111411-A-G
• rs247008

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.431 AC: 17892 AN: 41518

American (AMR) AF: 0.679 AC: 10376 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2255 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2435 AN: 5176

South Asian (SAS) AF: 0.613 AC: 2951 AN: 4816

European-Finnish (FIN) AF: 0.614 AC: 6487 AN: 10560

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.667 AC: 45354 AN: 67994

Other (OTH) AF: 0.620 AC: 1310 AN: 2112

Alfa AF: 0.648 Hom.: 105876

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
PhyloP100		0.078

Splicing

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

Other links and lift over

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