chr5-76846-C-G

Position:

• chr5-76846-C-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 0.373 in 152,030 control chromosomes in the GnomAD database, including 11,506 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 0.37 (11506 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 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: 0.373 AC: 56648 AN: 151912 Hom.: 11466 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.373 AC: 56731 AN: 152030 Hom.: 11506 Cov.: 33 AF XY: 0.370 AC XY: 27509 AN XY: 74316

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.341

Alfa AF: 0.355 Hom.: 1229

Bravo AF: 0.380

Asia WGS AF: 0.145 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6859237; hg19: chr5-76961;