NM_152381.6:c.563-26339G>A

Variant names:

• chr2-167184396-G-A
• rs10497320
• NM_152381.6:c.563-26339G>A

Variant summary

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

The NM_152381.6(XIRP2):​c.563-26339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0885 in 595,792 control chromosomes in the GnomAD database, including 2,797 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 0.080 (533 hom., cov: 32)
  • Exomes 𝑓: 0.092 (2264 hom.)
• Consequence: XIRP2 NM_152381.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 5 publications found

Genes affected

XIRP2 (HGNC:14303): (xin actin binding repeat containing 2) Enables actin filament binding activity. Predicted to be involved in actin cytoskeleton organization and heart development. Predicted to act upstream of or within cardiac muscle tissue morphogenesis; cell-cell junction organization; and ventricular septum development. Colocalizes with focal adhesion and stress fiber. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152381.6. 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
	XIRP2	NM_152381.6	MANE Select	c.563-26339G>A		intron	N/A	NP_689594.4
	XIRP2	NM_001199143.2		c.563-146G>A		intron	N/A	NP_001186072.1
	XIRP2	NM_001079810.4		c.563-26339G>A		intron	N/A	NP_001073278.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XIRP2	ENST00000409195.6	TSL:5 MANE Select	c.563-26339G>A		intron	N/A	ENSP00000386840.2
	XIRP2	ENST00000409728.5	TSL:1	c.563-146G>A		intron	N/A	ENSP00000386619.1
	XIRP2	ENST00000409043.5	TSL:1	c.563-26339G>A		intron	N/A	ENSP00000386454.1

Frequencies

GnomAD3 genomes AF: 0.0796 AC: 12106 AN: 152030 Hom.: 530 Cov.: 32

Gnomad AFR AF: 0.0659

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.0982

GnomAD4 exome AF: 0.0915 AC: 40611 AN: 443644 Hom.: 2264 AF XY: 0.0969 AC XY: 22706 AN XY: 234214

African (AFR) AF: 0.0741 AC: 889 AN: 11998

American (AMR) AF: 0.0602 AC: 1019 AN: 16932

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 1710 AN: 13262

East Asian (EAS) AF: 0.0565 AC: 1719 AN: 30398

South Asian (SAS) AF: 0.167 AC: 6909 AN: 41476

European-Finnish (FIN) AF: 0.0422 AC: 1607 AN: 38066

Middle Eastern (MID) AF: 0.180 AC: 635 AN: 3522

European-Non Finnish (NFE) AF: 0.0899 AC: 23602 AN: 262546

Other (OTH) AF: 0.0991 AC: 2521 AN: 25444

GnomAD4 genome AF: 0.0796 AC: 12116 AN: 152148 Hom.: 533 Cov.: 32 AF XY: 0.0793 AC XY: 5897 AN XY: 74380

African (AFR) AF: 0.0661 AC: 2744 AN: 41516

American (AMR) AF: 0.0715 AC: 1092 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3466

East Asian (EAS) AF: 0.0774 AC: 401 AN: 5182

South Asian (SAS) AF: 0.155 AC: 746 AN: 4818

European-Finnish (FIN) AF: 0.0390 AC: 413 AN: 10602

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0864 AC: 5875 AN: 67984

Other (OTH) AF: 0.0971 AC: 204 AN: 2100

Alfa AF: 0.0834 Hom.: 212

Bravo AF: 0.0802

Asia WGS AF: 0.102 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.67
PhyloP100		-1.5
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: rs10497320; hg19: chr2-168040906;