19-33209539-C-T

Position:

• chr19-33209539-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_019849.3(SLC7A10):​c.1264-54G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 1,587,756 control chromosomes in the GnomAD database, including 236,779 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.43 (16629 hom., cov: 31)
  • Exomes 𝑓: 0.54 (220150 hom.)
• Consequence: SLC7A10 NM_019849.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0680

Genes affected

SLC7A10 (HGNC:11058): (solute carrier family 7 member 10) SLC7A10, in association with 4F2HC (SLC3A2; MIM 158070), mediates high-affinity transport of D-serine and several other neutral amino acids (Nakauchi et al., 2000 [PubMed 10863037]).[supplied by OMIM, Mar 2008]

SLC7A10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 19-33209539-C-T is Benign according to our data. Variant chr19-33209539-C-T is described in ClinVar as [Benign]. Clinvar id is 1241970.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A10	NM_019849.3	c.1264-54G>A		intron_variant		ENST00000253188.8	NP_062823.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A10	ENST00000253188.8	c.1264-54G>A		intron_variant		1	NM_019849.3	ENSP00000253188.2
SLC7A10	ENST00000590036.5	n.1167-54G>A		intron_variant		5		ENSP00000465421.1
SLC7A10	ENST00000590490.1	n.1039-54G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65865 AN: 151894 Hom.: 16627 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.466

GnomAD4 exome AF: 0.540 AC: 775812 AN: 1435744 Hom.: 220150 AF XY: 0.538 AC XY: 383670 AN XY: 713428

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.300

Gnomad4 ASJ exome AF: 0.569

Gnomad4 EAS exome AF: 0.0957

Gnomad4 SAS exome AF: 0.367

Gnomad4 FIN exome AF: 0.582

Gnomad4 NFE exome AF: 0.588

Gnomad4 OTH exome AF: 0.509

GnomAD4 genome AF: 0.433 AC: 65876 AN: 152012 Hom.: 16629 Cov.: 31 AF XY: 0.429 AC XY: 31851 AN XY: 74320

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.461

Alfa AF: 0.527 Hom.: 3493

Bravo AF: 0.405

Asia WGS AF: 0.221 AC: 766 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.43

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: rs2303093; hg19: chr19-33700445; COSMIC: COSV53502993; COSMIC: COSV53502993;