chr4-133550707-C-T

Variant names:

• chr4-133550707-C-T
• rs1493517
• ENST00000721553.1:n.142-1588C>T

Variant summary

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

The ENST00000721553.1(ENSG00000294158):​n.142-1588C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 151,956 control chromosomes in the GnomAD database, including 29,246 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 0.62 (29246 hom., cov: 32)
• Consequence: ENSG00000294158 ENST00000721553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 3 publications found

Genes affected

ENSG00000294158 (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 (EAS) allele frequency at 95% confidence interval = 0.707 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
ENSG00000294158	ENST00000721553.1	n.142-1588C>T		intron_variant	Intron 1 of 3
ENSG00000294158	ENST00000721554.1	n.142-1588C>T		intron_variant	Intron 1 of 2
ENSG00000294158	ENST00000721555.1	n.132-1588C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93942 AN: 151838 Hom.: 29224 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.619 AC: 94009 AN: 151956 Hom.: 29246 Cov.: 32 AF XY: 0.617 AC XY: 45834 AN XY: 74272

African (AFR) AF: 0.603 AC: 24997 AN: 41432

American (AMR) AF: 0.589 AC: 8977 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1894 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3762 AN: 5176

South Asian (SAS) AF: 0.489 AC: 2356 AN: 4820

European-Finnish (FIN) AF: 0.705 AC: 7428 AN: 10542

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42631 AN: 67958

Other (OTH) AF: 0.597 AC: 1262 AN: 2114

Alfa AF: 0.624 Hom.: 112606

Bravo AF: 0.615

Asia WGS AF: 0.619 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs1493517; hg19: chr4-134471862; COSMIC: COSV69626968;