8-2216912-T-C

Variant names:

• chr8-2216912-T-C
• rs1382608

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 0.557 in 151,966 control chromosomes in the GnomAD database, including 25,751 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 0.56 (25751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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: 0.557 AC: 84554 AN: 151848 Hom.: 25704 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.557 AC: 84657 AN: 151966 Hom.: 25751 Cov.: 32 AF XY: 0.548 AC XY: 40724 AN XY: 74276

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.514

Alfa AF: 0.470 Hom.: 11387

Bravo AF: 0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1382608; hg19: chr8-2164581;