8-83220780-A-T

Variant names:

• chr8-83220780-A-T
• rs2140014

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 0.9 in 151,978 control chromosomes in the GnomAD database, including 62,095 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 0.90 (62095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.958 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: 0.900 AC: 136698 AN: 151860 Hom.: 62068 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.900 AC: 136778 AN: 151978 Hom.: 62095 Cov.: 32 AF XY: 0.900 AC XY: 66859 AN XY: 74322

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.915

Alfa AF: 0.940 Hom.: 3268

Bravo AF: 0.887

Asia WGS AF: 0.877 AC: 3048 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.48
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2140014; hg19: chr8-84133015;