rs2044999

chr8-113786995-G-Achr8-113786995-G-T

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 0.603 in 151,686 control chromosomes in the GnomAD database, including 28,227 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 0.60 (28227 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91408 AN: 151568 Hom.: 28198 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.603 AC: 91491 AN: 151686 Hom.: 28227 Cov.: 31 AF XY: 0.598 AC XY: 44300 AN XY: 74104

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.612

Alfa AF: 0.630 Hom.: 61581

Bravo AF: 0.581

Asia WGS AF: 0.507 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2044999; hg19: chr8-114799224;