chr2-183898831-A-G

Position:

• chr2-183898831-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658526.1(ENSG00000286879):​n.882A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,218 control chromosomes in the GnomAD database, including 1,218 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 0.081 (1218 hom., cov: 32)
• Consequence: ENST00000658526.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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
	ENST00000658526.1	n.882A>G		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12312 AN: 152100 Hom.: 1209 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00547

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0811 AC: 12348 AN: 152218 Hom.: 1218 Cov.: 32 AF XY: 0.0839 AC XY: 6244 AN XY: 74426

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0256

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.0808

Gnomad4 SAS AF: 0.0561

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.00547

Gnomad4 OTH AF: 0.0605

Alfa AF: 0.0381 Hom.: 95

Bravo AF: 0.0803

Asia WGS AF: 0.0760 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1471777; hg19: chr2-184763558;