chr5-77996116-G-A

Position:

• chr5-77996116-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0449 in 152,246 control chromosomes in the GnomAD database, including 289 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 0.045 (289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.27

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0449 AC: 6836 AN: 152128 Hom.: 289 Cov.: 33

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0963

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0414

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0449 AC: 6839 AN: 152246 Hom.: 289 Cov.: 33 AF XY: 0.0463 AC XY: 3447 AN XY: 74444

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0963

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.0662

Gnomad4 FIN AF: 0.0289

Gnomad4 NFE AF: 0.0414

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0484 Hom.: 289

Bravo AF: 0.0510

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	20
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12655917; hg19: chr5-77291940;