rs17289605

chr3-170730248-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687934.1(ENSG00000289233):n.407T>C variant causes a non coding transcript exon 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: ENST00000687934.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC7A14-AS1	NR_135556.1	n.766+553T>C		intron_variant, non_coding_transcript_variant
LOC124906302	XR_007096159.1	n.268+3435A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687934.1	n.407T>C		non_coding_transcript_exon_variant	1/1
SLC7A14-AS1	ENST00000644993.1	n.293+22054T>C		intron_variant, non_coding_transcript_variant
	ENST00000658869.1	n.136+5678A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.0948

Gnomad4 FIN AF: 0.0486

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.101 Hom.: 494

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17289605; hg19: chr3-170448037;