ENST00000411542.1:n.352-122263C>T

Variant names:

• chr7-13514383-C-T
• rs13227425
• ENST00000411542.1:n.352-122263C>T

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.352-122263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,058 control chromosomes in the GnomAD database, including 3,984 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 0.20 (3984 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 4 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411542.1. 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
	ENSG00000229618	ENST00000411542.1	TSL:4	n.352-122263C>T		intron	N/A
	ENSG00000229618	ENST00000638964.1	TSL:5	n.724-122263C>T		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.723-122263C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30061 AN: 151940 Hom.: 3982 Cov.: 32

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0837

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.198 AC: 30053 AN: 152058 Hom.: 3984 Cov.: 32 AF XY: 0.194 AC XY: 14433 AN XY: 74312

African (AFR) AF: 0.0507 AC: 2104 AN: 41532

American (AMR) AF: 0.197 AC: 3008 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3468

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5178

South Asian (SAS) AF: 0.0838 AC: 404 AN: 4822

European-Finnish (FIN) AF: 0.298 AC: 3141 AN: 10544

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19700 AN: 67946

Other (OTH) AF: 0.217 AC: 458 AN: 2114

Alfa AF: 0.227 Hom.: 600

Bravo AF: 0.186

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.3
DANN	Benign	0.78
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs13227425; hg19: chr7-13554008;