2-183911721-C-T

Position:

• chr2-183911721-C-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 0.812 in 151,964 control chromosomes in the GnomAD database, including 50,477 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 0.81 (50477 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.183911721C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234172	ENST00000441026.1	n.103+7090C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123271 AN: 151846 Hom.: 50452 Cov.: 33

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.812 AC: 123348 AN: 151964 Hom.: 50477 Cov.: 33 AF XY: 0.809 AC XY: 60119 AN XY: 74272

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.818

Alfa AF: 0.837 Hom.: 6654

Bravo AF: 0.817

Asia WGS AF: 0.837 AC: 2896 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826133; hg19: chr2-184776448;