8-21316149-T-G

Position:

• chr8-21316149-T-G

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 0.703 in 152,156 control chromosomes in the GnomAD database, including 39,010 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 0.70 (39010 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21316149T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106805 AN: 152038 Hom.: 38955 Cov.: 33

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.703 AC: 106919 AN: 152156 Hom.: 39010 Cov.: 33 AF XY: 0.704 AC XY: 52389 AN XY: 74364

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.686

Alfa AF: 0.619 Hom.: 41722

Bravo AF: 0.726

Asia WGS AF: 0.796 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs898249; hg19: chr8-21173660;