ENST00000523627.1:n.164+19528C>T

Variant names:

• chr8-22709841-C-T
• rs11775096
• ENST00000523627.1:n.164+19528C>T

Variant summary

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

The ENST00000523627.1(ENSG00000253125):​n.164+19528C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,072 control chromosomes in the GnomAD database, including 5,846 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 0.26 (5846 hom., cov: 32)
• Consequence: ENSG00000253125 ENST00000523627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521
• Publications: 2 publications found

Genes affected

ENSG00000253125 (HGNC:58186):

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 (NFE) allele frequency at 95% confidence interval = 0.324 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
ENSG00000253125	ENST00000523627.1	n.164+19528C>T		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39137 AN: 151954 Hom.: 5840 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.257 AC: 39158 AN: 152072 Hom.: 5846 Cov.: 32 AF XY: 0.254 AC XY: 18866 AN XY: 74336

African (AFR) AF: 0.144 AC: 5971 AN: 41448

American (AMR) AF: 0.277 AC: 4229 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3466

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5190

South Asian (SAS) AF: 0.220 AC: 1060 AN: 4828

European-Finnish (FIN) AF: 0.286 AC: 3023 AN: 10574

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22299 AN: 67970

Other (OTH) AF: 0.277 AC: 584 AN: 2110

Alfa AF: 0.313 Hom.: 15123

Bravo AF: 0.250

Asia WGS AF: 0.131 AC: 457 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	2.5
DANN	Benign	0.75
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs11775096; hg19: chr8-22567354;