3-188052818-T-C

Variant names:

• chr3-188052818-T-C
• rs12633719
• ENST00000754169.1:n.177+15909T>C

Variant summary

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

The ENST00000754169.1(ENSG00000298263):​n.177+15909T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,096 control chromosomes in the GnomAD database, including 5,367 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 (5367 hom., cov: 32)
• Consequence: ENSG00000298263 ENST00000754169.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 9 publications found

Genes affected

ENSG00000298263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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
ENSG00000298263	ENST00000754169.1	n.177+15909T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39625 AN: 151978 Hom.: 5358 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.261 AC: 39674 AN: 152096 Hom.: 5367 Cov.: 32 AF XY: 0.261 AC XY: 19421 AN XY: 74362

African (AFR) AF: 0.262 AC: 10868 AN: 41480

American (AMR) AF: 0.282 AC: 4308 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1171 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2065 AN: 5152

South Asian (SAS) AF: 0.379 AC: 1828 AN: 4824

European-Finnish (FIN) AF: 0.177 AC: 1875 AN: 10582

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16838 AN: 67992

Other (OTH) AF: 0.265 AC: 558 AN: 2108

Alfa AF: 0.258 Hom.: 16322

Bravo AF: 0.266

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.30
DANN	Benign	0.29
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs12633719; hg19: chr3-187770606;