rs2069616

chr5-132072384-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 0.401 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.401 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

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.407

Alfa AF: 0.428 Hom.: 17638

Bravo AF: 0.415

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.0
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

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