rs666788

chr5-41579365-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 0.103 in 152,198 control chromosomes in the GnomAD database, including 938 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 0.10 (938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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: 0.103 AC: 15596 AN: 152078 Hom.: 935 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.0628

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.103 AC: 15601 AN: 152198 Hom.: 938 Cov.: 32 AF XY: 0.0997 AC XY: 7418 AN XY: 74412

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00406

Gnomad4 SAS AF: 0.0620

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0989 Hom.: 146

Bravo AF: 0.110

Asia WGS AF: 0.0500 AC: 174 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.1
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs666788; hg19: chr5-41579467;