chr3-170510573-A-G

Variant names:

• chr3-170510573-A-G
• rs10490805
• NM_020949.3:c.305-9228T>C

Variant summary

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

The NM_020949.3(SLC7A14):​c.305-9228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,108 control chromosomes in the GnomAD database, including 1,508 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 (1508 hom., cov: 32)
• Consequence: SLC7A14 NM_020949.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 2 publications found

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:):

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A14	NM_020949.3	c.305-9228T>C		intron_variant	Intron 2 of 7	ENST00000231706.6	NP_066000.2
SLC7A14-AS1	NR_135555.1	n.215+33700A>G		intron_variant	Intron 2 of 2
SLC7A14-AS1	NR_135556.1	n.215+33700A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A14	ENST00000231706.6	c.305-9228T>C		intron_variant	Intron 2 of 7	2	NM_020949.3	ENSP00000231706.4
ENSG00000285218	ENST00000486975.1	c.391+87246A>G		intron_variant	Intron 2 of 3	2		ENSP00000417434.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16672 AN: 151990 Hom.: 1501 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0132

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0692

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.110 AC: 16702 AN: 152108 Hom.: 1508 Cov.: 32 AF XY: 0.105 AC XY: 7828 AN XY: 74386

African (AFR) AF: 0.242 AC: 10020 AN: 41418

American (AMR) AF: 0.0639 AC: 977 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0130 AC: 63 AN: 4828

European-Finnish (FIN) AF: 0.0363 AC: 385 AN: 10604

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0692 AC: 4705 AN: 67992

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.0787 Hom.: 481

Bravo AF: 0.119

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.67
DANN	Benign	0.48
PhyloP100		-0.61
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10490805; hg19: chr3-170228362;