ENST00000691186.2:n.281+23148G>C

Variant names:

• chr3-30415036-G-C
• rs1994987
• ENST00000691186.2:n.281+23148G>C

Variant summary

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

The ENST00000691186.2(ENSG00000289450):​n.281+23148G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,868 control chromosomes in the GnomAD database, including 6,516 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 0.29 (6516 hom., cov: 32)
• Consequence: ENSG00000289450 ENST00000691186.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 5 publications found

Genes affected

ENSG00000289450 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691186.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289450	ENST00000691186.2		n.281+23148G>C		intron	N/A
	ENSG00000289450	ENST00000701024.2		n.353-21157G>C		intron	N/A
	ENSG00000227549	ENST00000813769.1		n.505+7224C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44172 AN: 151748 Hom.: 6516 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.291 AC: 44199 AN: 151868 Hom.: 6516 Cov.: 32 AF XY: 0.290 AC XY: 21489 AN XY: 74218

African (AFR) AF: 0.244 AC: 10110 AN: 41430

American (AMR) AF: 0.282 AC: 4292 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1173 AN: 3464

East Asian (EAS) AF: 0.361 AC: 1855 AN: 5136

South Asian (SAS) AF: 0.259 AC: 1244 AN: 4804

European-Finnish (FIN) AF: 0.275 AC: 2906 AN: 10570

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21661 AN: 67914

Other (OTH) AF: 0.296 AC: 624 AN: 2110

Alfa AF: 0.173 Hom.: 368

Bravo AF: 0.291

Asia WGS AF: 0.297 AC: 1034 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.58
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1994987; hg19: chr3-30456528;