rs17289605

Variant names:

• chr3-170730248-T-C
• rs17289605
• ENST00000486975.1:c.*44+22054T>C

Variant summary

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

The ENST00000486975.1(ENSG00000285218):​c.*44+22054T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0867 in 152,174 control chromosomes in the GnomAD database, including 790 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 0.087 (790 hom., cov: 32)
• Consequence: ENSG00000285218 ENST00000486975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 3 publications found

Genes affected

ENSG00000285218 (HGNC:):

SLC7A14-AS1 (HGNC:54092): (SLC7A14 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A14-AS1	NR_135556.1	n.766+553T>C		intron_variant	Intron 5 of 5
LOC124906302	XR_007096159.1	n.268+3435A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285218	ENST00000486975.1	c.*44+22054T>C		intron_variant	Intron 3 of 3	2		ENSP00000417434.1

Frequencies

GnomAD3 genomes AF: 0.0868 AC: 13201 AN: 152056 Hom.: 791 Cov.: 32

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.0953

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.0867 AC: 13190 AN: 152174 Hom.: 790 Cov.: 32 AF XY: 0.0871 AC XY: 6483 AN XY: 74418

African (AFR) AF: 0.0248 AC: 1029 AN: 41532

American (AMR) AF: 0.160 AC: 2437 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 394 AN: 3468

East Asian (EAS) AF: 0.182 AC: 939 AN: 5170

South Asian (SAS) AF: 0.0948 AC: 457 AN: 4822

European-Finnish (FIN) AF: 0.0486 AC: 515 AN: 10606

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7001 AN: 67980

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.101 Hom.: 676

Bravo AF: 0.0931

Asia WGS AF: 0.126 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17289605; hg19: chr3-170448037;