rs1469096224

Variant names:

• chr17-46297565-C-G
• rs1469096224
• NM_014834.4:c.2432C>G

Your query was ambiguous. Multiple possible variants found:

• chr17-46297565-C-G
• chr17-46297565-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_014834.4(LRRC37A):​c.2432C>G​(p.Thr811Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T811I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 7)
  • Exomes 𝑓: 0.0000022 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LRRC37A NM_014834.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

Genes affected

LRRC37A (HGNC:29069): (leucine rich repeat containing 37A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ARL17B (HGNC:32387): (ADP ribosylation factor like GTPase 17B) Predicted to enable GTP binding activity. Predicted to be involved in intracellular protein transport and vesicle-mediated transport. Predicted to be located in Golgi apparatus. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.026102602).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC37A	NM_014834.4	c.2432C>G	p.Thr811Ser	missense_variant	Exon 1 of 14	ENST00000320254.5	NP_055649.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC37A	ENST00000320254.5	c.2432C>G	p.Thr811Ser	missense_variant	Exon 1 of 14	1	NM_014834.4	ENSP00000326324.5

Frequencies

GnomAD3 genomes Cov.: 7

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000216 AC: 1 AN: 464024 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 248918

Gnomad4 AFR exome AF: 0.0000717

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 7

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.092
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	0.18
DANN	Benign	0.27
DEOGEN2	Benign	0.0014	.;T
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.0012	N
LIST_S2	Benign	0.17	T;T
M_CAP	Benign	0.0016	T
MetaRNN	Benign	0.026	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.16	.;N
PrimateAI	Uncertain	0.49	T
PROVEAN	Benign	-0.91	N;N
REVEL	Benign	0.076
Sift	Benign	0.97	T;T
Sift4G	Benign	0.56	T;T
Polyphen		0.0	.;B
Vest4		0.055
MutPred		0.15		Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);
MVP		0.043
ClinPred		0.025	T
GERP RS		-3.0
Varity_R		0.032
gMVP		0.046

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: rs1469096224; hg19: chr17-44374931;