rs16869977

chr5-40407216-G-A

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 0.0858 in 152,202 control chromosomes in the GnomAD database, including 790 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 0.086 (790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 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: 0.0857 AC: 13030 AN: 152084 Hom.: 781 Cov.: 32

Gnomad AFR AF: 0.0485

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0590

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.0858 AC: 13063 AN: 152202 Hom.: 790 Cov.: 32 AF XY: 0.0856 AC XY: 6372 AN XY: 74408

Gnomad4 AFR AF: 0.0486

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.0901

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0597

Gnomad4 FIN AF: 0.0448

Gnomad4 NFE AF: 0.0901

Gnomad4 OTH AF: 0.0894

Alfa AF: 0.0868 Hom.: 290

Bravo AF: 0.0995

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.6
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16869977; hg19: chr5-40407318;