2-183294308-A-G

Position:

• chr2-183294308-A-G

Variant summary

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

The ENST00000653710.1(ENSG00000287621):​n.170-22447A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,966 control chromosomes in the GnomAD database, including 14,141 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 0.41 (14141 hom., cov: 31)
• Consequence: ENST00000653710.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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
	ENST00000653710.1	n.170-22447A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62900 AN: 151848 Hom.: 14144 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.414 AC: 62912 AN: 151966 Hom.: 14141 Cov.: 31 AF XY: 0.418 AC XY: 31028 AN XY: 74242

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.404

Alfa AF: 0.460 Hom.: 24709

Bravo AF: 0.385

Asia WGS AF: 0.519 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11683501; hg19: chr2-184159036;