11-124123301-T-G

Variant names:

• chr11-124123301-T-G
• rs880321
• NM_001130142.2:c.931-65T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001130142.2(VWA5A):​c.931-65T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000719 in 1,390,212 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: VWA5A NM_001130142.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• Publications: 0 publications found

Genes affected

VWA5A (HGNC:6658): (von Willebrand factor A domain containing 5A) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130142.2. 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
	VWA5A	NM_001130142.2	MANE Select	c.931-65T>G		intron	N/A	NP_001123614.1
	VWA5A	NM_014622.5		c.931-65T>G		intron	N/A	NP_055437.2
	VWA5A	NM_198315.3		c.931-65T>G		intron	N/A	NP_938057.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VWA5A	ENST00000456829.7	TSL:1 MANE Select	c.931-65T>G		intron	N/A	ENSP00000407726.2
	VWA5A	ENST00000392748.5	TSL:1	c.931-65T>G		intron	N/A	ENSP00000376504.1
	VWA5A	ENST00000361352.9	TSL:1	c.931-65T>G		intron	N/A	ENSP00000355070.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.19e-7 AC: 1 AN: 1390212 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 693446

African (AFR) AF: 0.00 AC: 0 AN: 31076

American (AMR) AF: 0.00 AC: 0 AN: 38742

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24566

East Asian (EAS) AF: 0.00 AC: 0 AN: 39382

South Asian (SAS) AF: 0.00 AC: 0 AN: 80926

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51732

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5564

European-Non Finnish (NFE) AF: 9.43e-7 AC: 1 AN: 1060476

Other (OTH) AF: 0.00 AC: 0 AN: 57748

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.59
PhyloP100		0.58

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: rs880321; hg19: chr11-123994008;