rs891671

Variant names:

• chr9-33232273-C-A
• rs891671
• ENST00000379725.5:c.130+11165C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-33232273-C-A
• chr9-33232273-C-G
• chr9-33232273-C-T

Variant summary

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

The ENST00000379725.5(SPINK4):​c.130+11165C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,060 control chromosomes in the GnomAD database, including 43,277 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 0.73 (43277 hom., cov: 31)
• Consequence: SPINK4 ENST00000379725.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.786
• Publications: 2 publications found

Genes affected

SPINK4 (HGNC:16646): (serine peptidase inhibitor Kazal type 4) Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of endopeptidase activity and response to xenobiotic stimulus. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000379725.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPINK4	ENST00000379725.5	TSL:3	c.130+11165C>A		intron	N/A	ENSP00000369048.1

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111371 AN: 151942 Hom.: 43261 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.733 AC: 111422 AN: 152060 Hom.: 43277 Cov.: 31 AF XY: 0.739 AC XY: 54978 AN XY: 74350

African (AFR) AF: 0.449 AC: 18609 AN: 41432

American (AMR) AF: 0.824 AC: 12584 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2921 AN: 3472

East Asian (EAS) AF: 0.865 AC: 4472 AN: 5170

South Asian (SAS) AF: 0.792 AC: 3823 AN: 4824

European-Finnish (FIN) AF: 0.866 AC: 9158 AN: 10578

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57192 AN: 67988

Other (OTH) AF: 0.747 AC: 1577 AN: 2112

Alfa AF: 0.793 Hom.: 18767

Bravo AF: 0.718

Asia WGS AF: 0.782 AC: 2722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.66
PhyloP100		0.79
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs891671; hg19: chr9-33232271;