8-82016363-T-C

Position:

• chr8-82016363-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 0.373 in 152,004 control chromosomes in the GnomAD database, including 10,716 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 0.37 (10716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 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: 0.373 AC: 56597 AN: 151886 Hom.: 10705 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.373 AC: 56643 AN: 152004 Hom.: 10716 Cov.: 32 AF XY: 0.367 AC XY: 27294 AN XY: 74296

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.389

Alfa AF: 0.360 Hom.: 4497

Bravo AF: 0.383

Asia WGS AF: 0.338 AC: 1174 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7820074; hg19: chr8-82928598; COSMIC: COSV54983742;