rs17353301

Variant names:

• chr4-33811267-A-G
• rs17353301
• ENST00000512581.5:n.165-34645T>C

Variant summary

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

The ENST00000512581.5(ENSG00000250954):​n.165-34645T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,190 control chromosomes in the GnomAD database, including 1,384 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 (1384 hom., cov: 32)
• Consequence: ENSG00000250954 ENST00000512581.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 2 publications found

Genes affected

ENSG00000250954 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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
ENSG00000250954	ENST00000512581.5	n.165-34645T>C		intron_variant	Intron 2 of 2	3
ENSG00000250954	ENST00000664054.1	n.264+358T>C		intron_variant	Intron 3 of 3
ENSG00000250954	ENST00000773638.1	n.267+358T>C		intron_variant	Intron 3 of 3
ENSG00000250954	ENST00000773639.1	n.*166T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17341 AN: 152068 Hom.: 1384 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.114 AC: 17332 AN: 152190 Hom.: 1384 Cov.: 32 AF XY: 0.111 AC XY: 8265 AN XY: 74394

African (AFR) AF: 0.0273 AC: 1133 AN: 41558

American (AMR) AF: 0.101 AC: 1541 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3470

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5160

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4828

European-Finnish (FIN) AF: 0.165 AC: 1749 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11620 AN: 67982

Other (OTH) AF: 0.142 AC: 300 AN: 2112

Alfa AF: 0.147 Hom.: 3105

Bravo AF: 0.110

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.51
PhyloP100		0.54
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: rs17353301; hg19: chr4-33812889;