8-21381562-A-T

Variant names:

• chr8-21381562-A-T
• rs4382469

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 0.521 in 152,118 control chromosomes in the GnomAD database, including 21,447 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 0.52 (21447 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 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: 0.521 AC: 79176 AN: 152000 Hom.: 21425 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.521 AC: 79247 AN: 152118 Hom.: 21447 Cov.: 33 AF XY: 0.517 AC XY: 38474 AN XY: 74362

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.557

Alfa AF: 0.406 Hom.: 1122

Bravo AF: 0.518

Asia WGS AF: 0.471 AC: 1640 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	0.012
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4382469; hg19: chr8-21239073;