chr19-33208758-T-TA

Position:

• chr19-33208758-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002333.4(LRP3):​c.*1186dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.81 (50292 hom., cov: 0)
  • Exomes 𝑓: 0.86 (414996 hom.)
• Consequence: LRP3 NM_002333.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.274

Genes affected

LRP3 (HGNC:6695): (LDL receptor related protein 3) Involved in negative regulation of fat cell differentiation; positive regulation of osteoblast differentiation; and regulation of gene expression. Predicted to be located in clathrin-coated pit. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 -10 ACMG points.

• BP6: Variant 19-33208758-T-TA is Benign according to our data. Variant chr19-33208758-T-TA is described in ClinVar as [Benign]. Clinvar id is 1294937.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRP3	NM_002333.4	c.*1186dupA		3_prime_UTR_variant	7/7	ENST00000253193.9	NP_002324.2
SLC7A10	NM_019849.3	c.*132dupT		3_prime_UTR_variant	11/11	ENST00000253188.8	NP_062823.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRP3	ENST00000253193.9	c.*1186dupA		3_prime_UTR_variant	7/7	1	NM_002333.4	ENSP00000253193.6
SLC7A10	ENST00000253188.8	c.*132dupT		3_prime_UTR_variant	11/11	1	NM_019849.3	ENSP00000253188.2
SLC7A10	ENST00000590490.1	n.*17dupT		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122711 AN: 152046 Hom.: 50254 Cov.: 0

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.831

GnomAD4 exome AF: 0.860 AC: 953010 AN: 1107532 Hom.: 414996 Cov.: 15 AF XY: 0.861 AC XY: 480666 AN XY: 558284

Gnomad4 AFR exome AF: 0.699

Gnomad4 AMR exome AF: 0.804

Gnomad4 ASJ exome AF: 0.879

Gnomad4 EAS exome AF: 0.460

Gnomad4 SAS exome AF: 0.851

Gnomad4 FIN exome AF: 0.809

Gnomad4 NFE exome AF: 0.889

Gnomad4 OTH exome AF: 0.839

GnomAD4 genome AF: 0.807 AC: 122805 AN: 152164 Hom.: 50292 Cov.: 0 AF XY: 0.803 AC XY: 59741 AN XY: 74376

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.825

Alfa AF: 0.844 Hom.: 6637

Bravo AF: 0.798

Asia WGS AF: 0.663 AC: 2306 AN: 3476

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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs57394649; hg19: chr19-33699664;