8-2216912-T-C

Position:

• chr8-2216912-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;