chr5-132072384-A-G

Variant names:

• chr5-132072384-A-G
• rs2069616

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 0.401 in 152,104 control chromosomes in the GnomAD database, including 13,111 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 0.40 (13111 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.401 AC: 61010 AN: 151986 Hom.: 13096 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.401 AC: 61049 AN: 152104 Hom.: 13111 Cov.: 33 AF XY: 0.385 AC XY: 28626 AN XY: 74378

African (AFR) AF: 0.495 AC: 20528 AN: 41466

American (AMR) AF: 0.347 AC: 5299 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1181 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5182

South Asian (SAS) AF: 0.128 AC: 617 AN: 4824

European-Finnish (FIN) AF: 0.276 AC: 2925 AN: 10588

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 28993 AN: 67974

Other (OTH) AF: 0.407 AC: 857 AN: 2104

Alfa AF: 0.427 Hom.: 33292

Bravo AF: 0.415

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.76
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs2069616; hg19: chr5-131408077; COSMIC: COSV51522282;