chr8-142918184-A-G

Variant names:

• chr8-142918184-A-G
• rs1799998

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.387 in 151,942 control chromosomes in the GnomAD database, including 12,316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.39 (12316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.134
• Publications: 382 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 8-142918184-A-G is Benign according to our data. Variant chr8-142918184-A-G is described in ClinVar as Benign. ClinVar VariationId is 759405.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.387 AC: 58808 AN: 151824 Hom.: 12317 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.387 AC: 58817 AN: 151942 Hom.: 12316 Cov.: 32 AF XY: 0.392 AC XY: 29148 AN XY: 74288

African (AFR) AF: 0.229 AC: 9470 AN: 41428

American (AMR) AF: 0.431 AC: 6585 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1879 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1551 AN: 5158

South Asian (SAS) AF: 0.421 AC: 2025 AN: 4814

European-Finnish (FIN) AF: 0.485 AC: 5106 AN: 10538

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30733 AN: 67950

Other (OTH) AF: 0.413 AC: 871 AN: 2108

Alfa AF: 0.418 Hom.: 38072

Bravo AF: 0.376

Asia WGS AF: 0.317 AC: 1104 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.5
DANN	Benign	0.89
PhyloP100		-0.13
PromoterAI		-0.013	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1799998; hg19: chr8-143999600;