rs6706115

Variant names:

• chr2-167181483-T-A
• rs6706115
• NM_152381.6:c.563-29252T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-167181483-T-A
• chr2-167181483-T-C

Variant summary

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

The NM_152381.6(XIRP2):​c.563-29252T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 152,262 control chromosomes in the GnomAD database, including 795 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 0.099 (795 hom., cov: 32)
• Consequence: XIRP2 NM_152381.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XIRP2	NM_152381.6	c.563-29252T>A		intron_variant	Intron 3 of 10	ENST00000409195.6	NP_689594.4
XIRP2	NM_001199143.2	c.563-3059T>A		intron_variant	Intron 3 of 10		NP_001186072.1
XIRP2	NM_001079810.4	c.563-29252T>A		intron_variant	Intron 3 of 9		NP_001073278.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XIRP2	ENST00000409195.6	c.563-29252T>A		intron_variant	Intron 3 of 10	5	NM_152381.6	ENSP00000386840.2

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14979 AN: 152144 Hom.: 786 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0775

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0986 AC: 15010 AN: 152262 Hom.: 795 Cov.: 32 AF XY: 0.0966 AC XY: 7191 AN XY: 74460

African (AFR) AF: 0.132 AC: 5503 AN: 41550

American (AMR) AF: 0.0787 AC: 1203 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 425 AN: 3472

East Asian (EAS) AF: 0.0769 AC: 399 AN: 5186

South Asian (SAS) AF: 0.155 AC: 745 AN: 4814

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: 5880 AN: 68030

Other (OTH) AF: 0.107 AC: 225 AN: 2108

Alfa AF: 0.0437 Hom.: 29

Bravo AF: 0.102

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.34
PhyloP100		-0.55
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: rs6706115; hg19: chr2-168037993;