rs1799998

Positions:

• chr8-142918184-A-G
• chr8-142918184-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 id 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.

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: 0.387 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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.413

Alfa AF: 0.427 Hom.: 14122

Bravo AF: 0.376

Asia WGS AF: 0.317 AC: 1104 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799998; hg19: chr8-143999600;