8-5183895-C-T

Variant names:

• chr8-5183895-C-T
• rs6989820

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 0.51 in 151,930 control chromosomes in the GnomAD database, including 20,870 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 0.51 (20870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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: 0.509 AC: 77340 AN: 151812 Hom.: 20831 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.510 AC: 77433 AN: 151930 Hom.: 20870 Cov.: 32 AF XY: 0.506 AC XY: 37546 AN XY: 74236

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.510

Alfa AF: 0.435 Hom.: 24583

Bravo AF: 0.521

Asia WGS AF: 0.470 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.95
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6989820; hg19: chr8-5041417;