chr19-33209172-C-T

Position:

• chr19-33209172-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_019849.3(SLC7A10):​c.1441+136G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 1,506,498 control chromosomes in the GnomAD database, including 206,887 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.38 (14656 hom., cov: 32)
  • Exomes 𝑓: 0.51 (192231 hom.)
• Consequence: SLC7A10 NM_019849.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.942

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 19-33209172-C-T is Benign according to our data. Variant chr19-33209172-C-T is described in ClinVar as [Benign]. Clinvar id is 1289967.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A10	NM_019849.3	c.1441+136G>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.1441+136G>A		intron_variant		1	NM_019849.3	ENSP00000253188.2
SLC7A10	ENST00000590036.5	n.*174+136G>A		intron_variant		5		ENSP00000465421.1
SLC7A10	ENST00000590490.1	n.1216+136G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58000 AN: 151976 Hom.: 14655 Cov.: 32

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.405

GnomAD4 exome AF: 0.512 AC: 693019 AN: 1354404 Hom.: 192231 Cov.: 22 AF XY: 0.506 AC XY: 341272 AN XY: 674102

Gnomad4 AFR exome AF: 0.0795

Gnomad4 AMR exome AF: 0.269

Gnomad4 ASJ exome AF: 0.488

Gnomad4 EAS exome AF: 0.0111

Gnomad4 SAS exome AF: 0.279

Gnomad4 FIN exome AF: 0.598

Gnomad4 NFE exome AF: 0.570

Gnomad4 OTH exome AF: 0.460

GnomAD4 genome AF: 0.381 AC: 57987 AN: 152094 Hom.: 14656 Cov.: 32 AF XY: 0.377 AC XY: 28022 AN XY: 74354

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.400

Alfa AF: 0.491 Hom.: 5909

Bravo AF: 0.347

Asia WGS AF: 0.132 AC: 460 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 16, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.55
DANN	Benign	0.53

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: rs11671790; hg19: chr19-33700078;