8-65087728-C-T

Variant names:

• chr8-65087728-C-T
• rs2980003

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 0.267 in 152,074 control chromosomes in the GnomAD database, including 5,509 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 0.27 (5509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

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 (EAS) allele frequency at 95% confidence interval = 0.372 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: 0.267 AC: 40602 AN: 151956 Hom.: 5496 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.267 AC: 40641 AN: 152074 Hom.: 5509 Cov.: 32 AF XY: 0.270 AC XY: 20086 AN XY: 74332

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.276

Alfa AF: 0.267 Hom.: 3722

Bravo AF: 0.271

Asia WGS AF: 0.340 AC: 1183 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	4.8
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: rs2980003; hg19: chr8-65999963;