2-199130145-T-C

Variant names:

• chr2-199130145-T-C
• rs1451487
• ENST00000827186.1:n.131-28419A>G

Variant summary

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

The ENST00000827186.1(ENSG00000307577):​n.131-28419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,126 control chromosomes in the GnomAD database, including 2,148 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 0.16 (2148 hom., cov: 32)
• Consequence: ENSG00000307577 ENST00000827186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.832
• Publications: 2 publications found

Genes affected

ENSG00000307577 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827186.1. 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
	ENSG00000307577	ENST00000827186.1		n.131-28419A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24748 AN: 152008 Hom.: 2145 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.163 AC: 24761 AN: 152126 Hom.: 2148 Cov.: 32 AF XY: 0.159 AC XY: 11848 AN XY: 74380

African (AFR) AF: 0.136 AC: 5651 AN: 41488

American (AMR) AF: 0.213 AC: 3259 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 588 AN: 3464

East Asian (EAS) AF: 0.315 AC: 1626 AN: 5162

South Asian (SAS) AF: 0.117 AC: 566 AN: 4822

European-Finnish (FIN) AF: 0.0898 AC: 951 AN: 10594

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11577 AN: 68006

Other (OTH) AF: 0.186 AC: 392 AN: 2110

Alfa AF: 0.162 Hom.: 1114

Bravo AF: 0.175

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.56
PhyloP100		0.83

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: rs1451487;

hg19: chr2-199994868;