chr2-183294308-A-G

Variant names:

• chr2-183294308-A-G
• rs11683501
• ENST00000653710.1:n.170-22447A>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 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: ENSG00000287621 ENST00000653710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

ENSG00000287621 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287621	ENST00000653710.1	n.170-22447A>G		intron_variant	Intron 1 of 3

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;