8-5213890-T-C

Variant names:

• chr8-5213890-T-C
• rs7816936

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;