ENST00000668357.1:n.293+4241C>T

Variant names:

• chr7-25427669-G-A
• rs17310121
• ENST00000668357.1:n.293+4241C>T

Variant summary

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

The ENST00000668357.1(ENSG00000233824):​n.293+4241C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,144 control chromosomes in the GnomAD database, including 400 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 0.067 (400 hom., cov: 32)
• Consequence: ENSG00000233824 ENST00000668357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 2 publications found

Genes affected

ENSG00000233824 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0861 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
ENSG00000233824	ENST00000668357.1	n.293+4241C>T		intron_variant	Intron 1 of 2
ENSG00000233824	ENST00000669800.2	n.294+4241C>T		intron_variant	Intron 1 of 1
ENSG00000233824	ENST00000718235.1	n.282+4241C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0669 AC: 10166 AN: 152026 Hom.: 400 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.0668 AC: 10170 AN: 152144 Hom.: 400 Cov.: 32 AF XY: 0.0655 AC XY: 4872 AN XY: 74360

African (AFR) AF: 0.0370 AC: 1538 AN: 41526

American (AMR) AF: 0.0681 AC: 1040 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5178

South Asian (SAS) AF: 0.0301 AC: 145 AN: 4824

European-Finnish (FIN) AF: 0.0705 AC: 746 AN: 10582

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5979 AN: 67980

Other (OTH) AF: 0.0858 AC: 181 AN: 2110

Alfa AF: 0.0861 Hom.: 1023

Bravo AF: 0.0667

Asia WGS AF: 0.0180 AC: 64 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.64
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs17310121; hg19: chr7-25467288;