ENST00000412413.1:n.128+1622G>T

Variant names:

• chr7-27363592-G-T
• rs9332393
• ENST00000412413.1:n.128+1622G>T

Variant summary

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

The ENST00000412413.1(ENSG00000224322):​n.128+1622G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,780 control chromosomes in the GnomAD database, including 6,178 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 0.28 (6178 hom., cov: 32)
• Consequence: ENSG00000224322 ENST00000412413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 1 publications found

Genes affected

ENSG00000224322 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224322	ENST00000412413.1	n.128+1622G>T		intron_variant	Intron 1 of 4	5
ENSG00000224322	ENST00000656126.2	n.65+1900G>T		intron_variant	Intron 1 of 4
ENSG00000224322	ENST00000664129.1	n.102+1900G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42432 AN: 151662 Hom.: 6175 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.280 AC: 42479 AN: 151780 Hom.: 6178 Cov.: 32 AF XY: 0.284 AC XY: 21028 AN XY: 74162

African (AFR) AF: 0.339 AC: 14026 AN: 41336

American (AMR) AF: 0.327 AC: 4989 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2649 AN: 5146

South Asian (SAS) AF: 0.270 AC: 1304 AN: 4822

European-Finnish (FIN) AF: 0.245 AC: 2572 AN: 10494

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14847 AN: 67954

Other (OTH) AF: 0.296 AC: 625 AN: 2110

Alfa AF: 0.147 Hom.: 278

Bravo AF: 0.291

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.66
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs9332393; hg19: chr7-27403211;