5-148171857-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001325.2(SPINK14):​c.111+884G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,750 control chromosomes in the GnomAD database, including 23,917 homozygotes. 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: 𝑓 0.56 (23917 hom., cov: 31)
• Consequence: SPINK14 NM_001001325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPINK14	NM_001001325.2	c.111+884G>C		intron_variant	Intron 3 of 4	ENST00000356972.2	NP_001001325.1
SPINK14	XM_017009469.2	c.111+884G>C		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>C		intron_variant	Intron 3 of 4	1	NM_001001325.2	ENSP00000349459.1
SPINK14	ENST00000562793.5	c.111+884G>C		intron_variant	Intron 2 of 2	5		ENSP00000457038.1
FBXO38-DT	ENST00000667608.1	n.1257-78115C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84508 AN: 151632 Hom.: 23896 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.557 AC: 84573 AN: 151750 Hom.: 23917 Cov.: 31 AF XY: 0.556 AC XY: 41210 AN XY: 74100

African (AFR) AF: 0.606 AC: 25092 AN: 41374

American (AMR) AF: 0.477 AC: 7259 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3470

East Asian (EAS) AF: 0.415 AC: 2128 AN: 5132

South Asian (SAS) AF: 0.524 AC: 2518 AN: 4806

European-Finnish (FIN) AF: 0.553 AC: 5825 AN: 10532

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.555 AC: 37699 AN: 67916

Other (OTH) AF: 0.568 AC: 1199 AN: 2112

Alfa AF: 0.553 Hom.: 2804

Bravo AF: 0.551

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.44
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1029884; hg19: chr5-147551420;