ENST00000421121.5:n.113+54349A>G

Variant names:

• chr7-11307574-A-G
• rs10486124
• ENST00000421121.5:n.113+54349A>G

Variant summary

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

The ENST00000421121.5(ENSG00000230333):​n.113+54349A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.07 in 152,200 control chromosomes in the GnomAD database, including 806 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 0.070 (806 hom., cov: 32)
• Consequence: ENSG00000230333 ENST00000421121.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.726
• Publications: 1 publications found

Genes affected

ENSG00000230333 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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
ENSG00000230333	ENST00000421121.5	n.113+54349A>G		intron_variant	Intron 1 of 2	1
ENSG00000230333	ENST00000428533.5	n.139-71713A>G		intron_variant	Intron 1 of 2	5
ENSG00000230333	ENST00000428967.5	n.497+59199A>G		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0701 AC: 10666 AN: 152082 Hom.: 808 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0586

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0700 AC: 10659 AN: 152200 Hom.: 806 Cov.: 32 AF XY: 0.0755 AC XY: 5615 AN XY: 74404

African (AFR) AF: 0.0144 AC: 600 AN: 41542

American (AMR) AF: 0.130 AC: 1986 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1976 AN: 5174

South Asian (SAS) AF: 0.111 AC: 537 AN: 4822

European-Finnish (FIN) AF: 0.110 AC: 1167 AN: 10586

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0586 AC: 3983 AN: 67994

Other (OTH) AF: 0.0714 AC: 151 AN: 2114

Alfa AF: 0.0645 Hom.: 51

Bravo AF: 0.0717

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.95
DANN	Benign	0.74
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs10486124; hg19: chr7-11347201;