rs696891

chr5-61608734-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 0.575 in 152,096 control chromosomes in the GnomAD database, including 27,622 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 0.58 (27622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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: 0.575 AC: 87417 AN: 151980 Hom.: 27587 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.575 AC: 87495 AN: 152096 Hom.: 27622 Cov.: 32 AF XY: 0.563 AC XY: 41902 AN XY: 74364

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.551

Alfa AF: 0.521 Hom.: 3804

Bravo AF: 0.589

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	18
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs696891; hg19: chr5-60904561;