8-5213890-T-C

Position:

• chr8-5213890-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 0.515 in 151,878 control chromosomes in the GnomAD database, including 20,957 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 0.52 (20957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 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: 0.515 AC: 78219 AN: 151758 Hom.: 20956 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.515 AC: 78248 AN: 151878 Hom.: 20957 Cov.: 32 AF XY: 0.506 AC XY: 37595 AN XY: 74246

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.562

Alfa AF: 0.556 Hom.: 22734

Bravo AF: 0.516

Asia WGS AF: 0.308 AC: 1070 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7816936; hg19: chr8-5071412;