ENST00000435148.1:n.591-12178C>T

Variant names:

• chr7-69236985-G-A
• rs12667374
• ENST00000435148.1:n.591-12178C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435148.1(ENSG00000225718):​n.591-12178C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0311 in 152,294 control chromosomes in the GnomAD database, including 109 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 0.031 (109 hom., cov: 32)
• Consequence: ENSG00000225718 ENST00000435148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449

Genes affected

ENSG00000225718 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.0565 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
ENSG00000225718	ENST00000435148.1	n.591-12178C>T		intron_variant	Intron 2 of 2	3
ENSG00000225718	ENST00000670444.1	n.530+34980C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0311 AC: 4736 AN: 152176 Hom.: 110 Cov.: 32

Gnomad AFR AF: 0.00960

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.00892

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0311 AC: 4733 AN: 152294 Hom.: 109 Cov.: 32 AF XY: 0.0292 AC XY: 2177 AN XY: 74466

Gnomad4 AFR AF: 0.00957

Gnomad4 AMR AF: 0.0314

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.0621

Gnomad4 SAS AF: 0.00851

Gnomad4 FIN AF: 0.0208

Gnomad4 NFE AF: 0.0466

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.0416 Hom.: 89

Bravo AF: 0.0325

Asia WGS AF: 0.0370 AC: 128 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	7.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12667374; hg19: chr7-68701972;