rs1029884

Variant names:

• chr5-148171857-G-A
• rs1029884
• NM_001001325.2:c.111+884G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-148171857-G-A
• chr5-148171857-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001001325.2(SPINK14):​c.111+884G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SPINK14 NM_001001325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

Genes affected

SPINK14 (HGNC:33825): (serine peptidase inhibitor Kazal type 14 (putative)) Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of endopeptidase activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

FBXO38-DT (HGNC:55589): (FBXO38 divergent transcript)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPINK14	NM_001001325.2	c.111+884G>A		intron_variant	Intron 3 of 4	ENST00000356972.2	NP_001001325.1
SPINK14	XM_017009469.2	c.111+884G>A		intron_variant	Intron 2 of 3		XP_016864958.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPINK14	ENST00000356972.2	c.111+884G>A		intron_variant	Intron 3 of 4	1	NM_001001325.2	ENSP00000349459.1
SPINK14	ENST00000562793.5	c.111+884G>A		intron_variant	Intron 2 of 2	5		ENSP00000457038.1
FBXO38-DT	ENST00000667608.1	n.1257-78115C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.8
DANN	Benign	0.92

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: rs1029884; hg19: chr5-147551420;