chr5-57781077-A-G

Position:

• chr5-57781077-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 0.0798 in 152,218 control chromosomes in the GnomAD database, including 866 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 0.080 (866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 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: 0.0795 AC: 12096 AN: 152100 Hom.: 855 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0826

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0361

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0798 AC: 12149 AN: 152218 Hom.: 866 Cov.: 32 AF XY: 0.0801 AC XY: 5962 AN XY: 74432

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.0362

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0835

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0361

Gnomad4 OTH AF: 0.0657

Alfa AF: 0.0422 Hom.: 351

Bravo AF: 0.0828

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6865443; hg19: chr5-57076904;