2-184188055-T-C

Variant names:

• chr2-184188055-T-C
• rs10497643
• ENST00000787527.1:n.96-681A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000787527.1(ENSG00000286152):​n.96-681A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000286152 ENST00000787527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821
• Publications: 3 publications found

Genes affected

ENSG00000286152 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787527.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286152	ENST00000787527.1		n.96-681A>G		intron	N/A

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

African (AFR) AF: 0.120 AC: 4985 AN: 41490

American (AMR) AF: 0.545 AC: 8328 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2047 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2413 AN: 5152

South Asian (SAS) AF: 0.484 AC: 2330 AN: 4816

European-Finnish (FIN) AF: 0.515 AC: 5433 AN: 10540

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36836 AN: 67932

Other (OTH) AF: 0.446 AC: 941 AN: 2110

Alfa AF: 0.393 Hom.: 2013

Bravo AF: 0.411

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.71
PhyloP100		0.82

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10497643;

hg19: chr2-185052782;