chr2-184188055-T-C

Position:

• chr2-184188055-T-C

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 0.42 in 151,980 control chromosomes in the GnomAD database, including 16,215 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 0.42 (16215 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.184188055T>C		intergenic_region
LOC105373777	XR_923654.2	n.26-681A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63888 AN: 151864 Hom.: 16211 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.420 AC: 63892 AN: 151980 Hom.: 16215 Cov.: 32 AF XY: 0.420 AC XY: 31172 AN XY: 74242

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.446

Alfa AF: 0.404 Hom.: 2003

Bravo AF: 0.411

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497643; hg19: chr2-185052782;