chr3-170514619-A-G

Position:

• chr3-170514619-A-G

Variant summary

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

The NM_020949.3(SLC7A14):​c.304+12014T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,052 control chromosomes in the GnomAD database, including 16,221 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 0.45 (16221 hom., cov: 33)
• Consequence: SLC7A14 NM_020949.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

Genes affected

SLC7A14 (HGNC:29326): (solute carrier family 7 member 14) This gene is predicted to encode a glycosylated, cationic amino acid transporter protein with 14 transmembrane domains. This gene is primarily expressed in skin fibroblasts, neural tissue, and primary endothelial cells and its protein is predicted to mediate lysosomal uptake of cationic amino acids. Mutations in this gene are associated with autosomal recessive retinitis pigmentosa. In mice, this gene is expressed in the photoreceptor layer of the retina where its expression increases over the course of retinal development and persists in the mature retina. [provided by RefSeq, Apr 2014]

ENSG00000285218 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A14	NM_020949.3	c.304+12014T>C		intron_variant		ENST00000231706.6	NP_066000.2
SLC7A14-AS1	NR_135555.1	n.215+37746A>G		intron_variant
SLC7A14-AS1	NR_135556.1	n.215+37746A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A14	ENST00000231706.6	c.304+12014T>C		intron_variant		2	NM_020949.3	ENSP00000231706.4
ENSG00000285218	ENST00000486975.1	c.391+91292A>G		intron_variant		2		ENSP00000417434.1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68766 AN: 151934 Hom.: 16222 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.452 AC: 68776 AN: 152052 Hom.: 16221 Cov.: 33 AF XY: 0.454 AC XY: 33742 AN XY: 74308

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.468

Alfa AF: 0.491 Hom.: 2312

Bravo AF: 0.438

Asia WGS AF: 0.414 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7632718; hg19: chr3-170232408;