rs368711613

Variant names:

• chr14-99652285-C-A
• rs368711613
• NM_001127258.3:c.317C>A

Your query was ambiguous. Multiple possible variants found:

• chr14-99652285-C-A
• chr14-99652285-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001127258.3(HHIPL1):​c.317C>A​(p.Thr106Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: HHIPL1 NM_001127258.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.15

Genes affected

HHIPL1 (HGNC:19710): (HHIP like 1) This gene encodes a protein that belongs to the glucose/sorbosone dehydrogenase family. The encoded protein also contains a domain that binds folate and reduced folic acid derivatives. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HHIPL1	NM_001127258.3	c.317C>A	p.Thr106Lys	missense_variant	Exon 2 of 9	ENST00000330710.10	NP_001120730.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HHIPL1	ENST00000330710.10	c.317C>A	p.Thr106Lys	missense_variant	Exon 2 of 9	1	NM_001127258.3	ENSP00000330601.5
HHIPL1	ENST00000357223.2	c.317C>A	p.Thr106Lys	missense_variant	Exon 2 of 8	1		ENSP00000349757.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Uncertain	0.042	T
BayesDel_noAF	Benign	-0.18
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.031	T;.
Eigen	Uncertain	0.25
Eigen_PC	Benign	0.19
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.25	T;T
M_CAP	Benign	0.024	T
MetaRNN	Uncertain	0.73	D;D
MetaSVM	Benign	-0.96	T
MutationAssessor	Uncertain	2.6	M;M
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	-2.2	N;N
REVEL	Benign	0.18
Sift	Benign	0.20	T;T
Sift4G	Benign	0.56	T;T
Polyphen		0.92	P;P
Vest4		0.69
MutPred		0.47		Gain of methylation at T106 (P = 0.0199);Gain of methylation at T106 (P = 0.0199);
MVP		0.51
MPC		1.2
ClinPred		0.97	D
GERP RS		4.8
Varity_R		0.31
gMVP		0.70

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: rs368711613; hg19: chr14-100118622;