rs2213948

Variant names:

• chr1-158880164-G-A
• rs2213948
• ENST00000431627.1:n.384G>A

Variant summary

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

The ENST00000431627.1(PYHIN5P):​n.384G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 153,040 control chromosomes in the GnomAD database, including 1,489 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 0.13 (1482 hom., cov: 32)
  • Exomes 𝑓: 0.11 (7 hom.)
• Consequence: PYHIN5P ENST00000431627.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 0 publications found

Genes affected

PYHIN5P (HGNC:51820): (pyrin and HIN domain family member 5, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431627.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYHIN5P	ENST00000431627.1	TSL:6	n.384G>A		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20025 AN: 152070 Hom.: 1479 Cov.: 32

Gnomad AFR AF: 0.0631

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.138

GnomAD4 exome AF: 0.114 AC: 97 AN: 850 Hom.: 7 Cov.: 0 AF XY: 0.123 AC XY: 53 AN XY: 430

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.333 AC: 2 AN: 6

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.109 AC: 82 AN: 754

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.109 AC: 7 AN: 64

Other (OTH) AF: 0.150 AC: 3 AN: 20

GnomAD4 genome AF: 0.132 AC: 20025 AN: 152190 Hom.: 1482 Cov.: 32 AF XY: 0.134 AC XY: 9984 AN XY: 74394

African (AFR) AF: 0.0630 AC: 2615 AN: 41534

American (AMR) AF: 0.120 AC: 1830 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1318 AN: 5170

South Asian (SAS) AF: 0.146 AC: 704 AN: 4828

European-Finnish (FIN) AF: 0.149 AC: 1572 AN: 10584

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10790 AN: 68004

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.142 Hom.: 1005

Bravo AF: 0.128

Asia WGS AF: 0.188 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		-0.61

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2213948;

hg19: chr1-158849954;