8-13900057-T-C

Variant names:

• chr8-13900057-T-C
• rs2017470

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 0.473 in 151,564 control chromosomes in the GnomAD database, including 16,949 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 0.47 (16949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 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: 0.472 AC: 71557 AN: 151446 Hom.: 16926 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.473 AC: 71618 AN: 151564 Hom.: 16949 Cov.: 32 AF XY: 0.471 AC XY: 34855 AN XY: 74050

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.483

Alfa AF: 0.336 Hom.: 855

Bravo AF: 0.478

Asia WGS AF: 0.553 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.54
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2017470; hg19: chr8-13757566;