rs12990630

Variant names:

• chr2-18928665-C-T
• rs12990630
• ENST00000776740.1:n.310+9288C>T

Variant summary

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

The ENST00000776740.1(ENSG00000287284):​n.310+9288C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 152,134 control chromosomes in the GnomAD database, including 1,213 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 0.084 (1213 hom., cov: 32)
• Consequence: ENSG00000287284 ENST00000776740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 1 publications found

Genes affected

ENSG00000287284 (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 (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776740.1. 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
	ENSG00000287284	ENST00000776740.1		n.310+9288C>T		intron	N/A
	ENSG00000287284	ENST00000776741.1		n.267+9288C>T		intron	N/A
	ENSG00000287284	ENST00000776742.1		n.267+9288C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12769 AN: 152016 Hom.: 1202 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0842 AC: 12806 AN: 152134 Hom.: 1213 Cov.: 32 AF XY: 0.0802 AC XY: 5964 AN XY: 74380

African (AFR) AF: 0.231 AC: 9576 AN: 41474

American (AMR) AF: 0.0480 AC: 733 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00477 AC: 23 AN: 4820

European-Finnish (FIN) AF: 0.0142 AC: 151 AN: 10602

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0301 AC: 2048 AN: 68004

Other (OTH) AF: 0.0697 AC: 147 AN: 2110

Alfa AF: 0.0464 Hom.: 1228

Bravo AF: 0.0932

Asia WGS AF: 0.0170 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.57
PhyloP100		-0.27

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: rs12990630;

hg19: chr2-19109931;