NM_020196.3:c.522+262G>C

Variant names:

• chr19-7626981-C-G
• rs794083
• NM_020196.3:c.522+262G>C

Variant summary

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

The NM_020196.3(XAB2):​c.522+262G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,088 control chromosomes in the GnomAD database, including 29,717 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 0.62 (29717 hom., cov: 33)
• Consequence: XAB2 NM_020196.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 8 publications found

Genes affected

XAB2 (HGNC:14089): (XPA binding protein 2) Involved in mRNA splicing, via spliceosome; transcription, DNA-templated; and transcription-coupled nucleotide-excision repair. Located in nucleoplasm. Part of U2-type catalytic step 2 spliceosome. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020196.3. 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
	XAB2	NM_020196.3	MANE Select	c.522+262G>C		intron	N/A	NP_064581.2	Q9HCS7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XAB2	ENST00000358368.5	TSL:1 MANE Select	c.522+262G>C		intron	N/A	ENSP00000351137.3	Q9HCS7
	XAB2	ENST00000925818.1		c.552+232G>C		intron	N/A	ENSP00000595877.1
	XAB2	ENST00000925815.1		c.522+262G>C		intron	N/A	ENSP00000595874.1

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93964 AN: 151970 Hom.: 29678 Cov.: 33

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.618 AC: 94057 AN: 152088 Hom.: 29717 Cov.: 33 AF XY: 0.616 AC XY: 45790 AN XY: 74328

African (AFR) AF: 0.719 AC: 29835 AN: 41488

American (AMR) AF: 0.582 AC: 8894 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1782 AN: 5174

South Asian (SAS) AF: 0.466 AC: 2245 AN: 4822

European-Finnish (FIN) AF: 0.657 AC: 6935 AN: 10554

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40611 AN: 67996

Other (OTH) AF: 0.607 AC: 1280 AN: 2110

Alfa AF: 0.613 Hom.: 3584

Bravo AF: 0.619

Asia WGS AF: 0.457 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.36
PhyloP100		-0.071
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: rs794083; hg19: chr19-7691867;