ENST00000438070.2:n.348-9236G>A

Variant names:

• chr2-206854160-G-A
• rs12466917
• ENST00000438070.3:n.348-9236G>A

Variant summary

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

The ENST00000438070.3(ENSG00000229321):​n.348-9236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,060 control chromosomes in the GnomAD database, including 983 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 0.11 (983 hom., cov: 32)
• Consequence: ENSG00000229321 ENST00000438070.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 2 publications found

Genes affected

ENSG00000229321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438070.3. 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
	ENSG00000229321	ENST00000438070.3	TSL:3	n.348-9236G>A		intron	N/A
	ENSG00000229321	ENST00000658291.1		n.3035-9236G>A		intron	N/A
	ENSG00000229321	ENST00000658889.1		n.2974-25223G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16850 AN: 151942 Hom.: 980 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0880

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.111 AC: 16860 AN: 152060 Hom.: 983 Cov.: 32 AF XY: 0.109 AC XY: 8126 AN XY: 74318

African (AFR) AF: 0.129 AC: 5361 AN: 41466

American (AMR) AF: 0.0971 AC: 1484 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3470

East Asian (EAS) AF: 0.109 AC: 566 AN: 5178

South Asian (SAS) AF: 0.115 AC: 554 AN: 4820

European-Finnish (FIN) AF: 0.0880 AC: 929 AN: 10552

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7252 AN: 67978

Other (OTH) AF: 0.117 AC: 247 AN: 2116

Alfa AF: 0.0930 Hom.: 354

Bravo AF: 0.111

Asia WGS AF: 0.110 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.51
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12466917; hg19: chr2-207718884;