ENST00000523005.1:n.69+3626C>T

Variant names:

• chr5-172766674-C-T
• rs881811
• ENST00000523005.1:n.69+3626C>T

Variant summary

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

The ENST00000523005.1(ENSG00000253736):​n.69+3626C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,226 control chromosomes in the GnomAD database, including 1,263 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 0.11 (1263 hom., cov: 33)
• Consequence: ENSG00000253736 ENST00000523005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 1 publications found

Genes affected

ENSG00000253736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 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
ENSG00000253736	ENST00000523005.1	n.69+3626C>T		intron_variant	Intron 1 of 1	3
ENSG00000253295	ENST00000733736.1	n.461+41C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16273 AN: 152112 Hom.: 1255 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0479

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.107 AC: 16314 AN: 152226 Hom.: 1263 Cov.: 33 AF XY: 0.109 AC XY: 8129 AN XY: 74436

African (AFR) AF: 0.195 AC: 8110 AN: 41502

American (AMR) AF: 0.128 AC: 1951 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0554 AC: 192 AN: 3466

East Asian (EAS) AF: 0.284 AC: 1472 AN: 5176

South Asian (SAS) AF: 0.110 AC: 532 AN: 4828

European-Finnish (FIN) AF: 0.0496 AC: 526 AN: 10612

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0479 AC: 3257 AN: 68028

Other (OTH) AF: 0.111 AC: 234 AN: 2112

Alfa AF: 0.0695 Hom.: 218

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs881811; hg19: chr5-172193677;