8-56280473-C-T

Variant names:

• chr8-56280473-C-T
• rs13275320

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.208 in 152,112 control chromosomes in the GnomAD database, including 4,254 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 0.21 (4254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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: 0.207 AC: 31512 AN: 151994 Hom.: 4231 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.208 AC: 31574 AN: 152112 Hom.: 4254 Cov.: 32 AF XY: 0.205 AC XY: 15259 AN XY: 74390

African (AFR) AF: 0.382 AC: 15841 AN: 41448

American (AMR) AF: 0.181 AC: 2774 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3468

East Asian (EAS) AF: 0.0601 AC: 312 AN: 5188

South Asian (SAS) AF: 0.137 AC: 661 AN: 4820

European-Finnish (FIN) AF: 0.133 AC: 1408 AN: 10596

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9311 AN: 67992

Other (OTH) AF: 0.207 AC: 437 AN: 2108

Alfa AF: 0.165 Hom.: 2703

Bravo AF: 0.219

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.81
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13275320; hg19: chr8-57193032;