5-76769877-T-C

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 0.642 in 151,298 control chromosomes in the GnomAD database, including 31,915 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 0.64 (31915 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 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: 0.642 AC: 97077 AN: 151182 Hom.: 31884 Cov.: 29

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.642 AC: 97164 AN: 151298 Hom.: 31915 Cov.: 29 AF XY: 0.635 AC XY: 46882 AN XY: 73884

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.645

Alfa AF: 0.608 Hom.: 3587

Bravo AF: 0.660

Asia WGS AF: 0.642 AC: 2226 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.41
Dann	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs253088; hg19: chr5-76065702;