8-20019459-T-G

Variant names:

• chr8-20019459-T-G
• rs7007797

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0863 in 152,138 control chromosomes in the GnomAD database, including 599 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 0.086 (599 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.895
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0991 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0864 AC: 13130 AN: 152020 Hom.: 600 Cov.: 31

Gnomad AFR AF: 0.0581

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0901

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.0863 AC: 13124 AN: 152138 Hom.: 599 Cov.: 31 AF XY: 0.0859 AC XY: 6390 AN XY: 74390

African (AFR) AF: 0.0581 AC: 2413 AN: 41516

American (AMR) AF: 0.0753 AC: 1150 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3470

East Asian (EAS) AF: 0.102 AC: 528 AN: 5174

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4820

European-Finnish (FIN) AF: 0.0901 AC: 954 AN: 10594

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6872 AN: 67968

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

Alfa AF: 0.0935 Hom.: 1105

Bravo AF: 0.0828

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.81
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs7007797; hg19: chr8-19876970;