chr1-158962765-C-T

Variant names:

• chr1-158962765-C-T
• rs1101999
• NM_152501.5:c.1360-10882C>T

Variant summary

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

The NM_152501.5(PYHIN1):​c.1360-10882C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,172 control chromosomes in the GnomAD database, including 65,670 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 0.92 (65670 hom., cov: 30)
• Consequence: PYHIN1 NM_152501.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 23 publications found

Genes affected

PYHIN1 (HGNC:28894): (pyrin and HIN domain family member 1) The protein encoded by this gene belongs to the HIN-200 family of interferon-inducible proteins that share a 200-amino acid signature motif at their C-termini. HIN200 proteins are primarily nuclear and are involved in transcriptional regulation of genes important for cell cycle control, differentiation, and apoptosis. Downregulation of this gene is associated with breast cancer. This protein acts as a tumor suppressor by promoting ubiquitination and subsequent degradation of MDM2, which leads to stabilization of p53/TP53. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152501.5. 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
	PYHIN1	NM_152501.5	MANE Select	c.1360-10882C>T		intron	N/A	NP_689714.2
	PYHIN1	NM_198928.5		c.1333-10882C>T		intron	N/A	NP_945146.1
	PYHIN1	NM_198929.5		c.1360-13936C>T		intron	N/A	NP_945147.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYHIN1	ENST00000368140.6	TSL:1 MANE Select	c.1360-10882C>T		intron	N/A	ENSP00000357122.1
	PYHIN1	ENST00000368138.7	TSL:1	c.1333-10882C>T		intron	N/A	ENSP00000357120.3
	PYHIN1	ENST00000392254.6	TSL:1	c.1360-13936C>T		intron	N/A	ENSP00000376083.2

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140085 AN: 152054 Hom.: 65636 Cov.: 30

Gnomad AFR AF: 0.728

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.921 AC: 140173 AN: 152172 Hom.: 65670 Cov.: 30 AF XY: 0.924 AC XY: 68718 AN XY: 74392

African (AFR) AF: 0.727 AC: 30175 AN: 41480

American (AMR) AF: 0.970 AC: 14851 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.994 AC: 3450 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5156 AN: 5158

South Asian (SAS) AF: 0.998 AC: 4807 AN: 4816

European-Finnish (FIN) AF: 1.00 AC: 10616 AN: 10616

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67929 AN: 68010

Other (OTH) AF: 0.944 AC: 1991 AN: 2110

Alfa AF: 0.973 Hom.: 218013

Bravo AF: 0.911

Asia WGS AF: 0.977 AC: 3398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		0.28
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: rs1101999; hg19: chr1-158932555;