8-21490841-T-C

Variant names:

• chr8-21490841-T-C
• rs1426192

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 0.382 in 152,082 control chromosomes in the GnomAD database, including 13,136 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 0.38 (13136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 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: 0.382 AC: 58054 AN: 151964 Hom.: 13101 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.382 AC: 58150 AN: 152082 Hom.: 13136 Cov.: 32 AF XY: 0.379 AC XY: 28154 AN XY: 74342

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.393

Alfa AF: 0.303 Hom.: 7286

Bravo AF: 0.412

Asia WGS AF: 0.487 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1426192; hg19: chr8-21348352;