chr6-31287764-T-C

Variant names:

• chr6-31287764-T-C
• rs2524050
• ENST00000428639.1:n.1201A>G

Variant summary

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

The ENST00000428639.1(WASF5P):​n.1201A>G 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 0.104 in 152,796 control chromosomes in the GnomAD database, including 915 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 0.10 (905 hom., cov: 31)
  • Exomes 𝑓: 0.12 (10 hom.)
• Consequence: WASF5P ENST00000428639.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482
• Publications: 18 publications found

Genes affected

WASF5P (HGNC:21665): (WASP family member 5, pseudogene) This gene is a pseudogene belonging to the family of genes encoding Wiskott-Aldrich syndrome (WAS) proteins, which are involved in the transmission of signals to the actin cytoskeleton. Wiskott-Aldrich syndrome is a disease of the immune system. This pseudogene, which is apparently not transcribed, resembles the gene encoding the WAS protein family member 3, which is located on chromosome 13. [provided by RefSeq, Jul 2008]

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428639.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WASF5P	ENST00000428639.1	TSL:6	n.1201A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+16658T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15689 AN: 150754 Hom.: 906 Cov.: 31

Gnomad AFR AF: 0.0783

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.116

GnomAD4 exome AF: 0.119 AC: 229 AN: 1926 Hom.: 10 Cov.: 0 AF XY: 0.114 AC XY: 130 AN XY: 1142

African (AFR) AF: 0.100 AC: 3 AN: 30

American (AMR) AF: 0.167 AC: 8 AN: 48

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 1 AN: 6

East Asian (EAS) AF: 0.0588 AC: 2 AN: 34

South Asian (SAS) AF: 0.0862 AC: 5 AN: 58

European-Finnish (FIN) AF: 0.0714 AC: 19 AN: 266

Middle Eastern (MID) AF: 0.0419 AC: 17 AN: 406

European-Non Finnish (NFE) AF: 0.172 AC: 145 AN: 842

Other (OTH) AF: 0.123 AC: 29 AN: 236

GnomAD4 genome AF: 0.104 AC: 15686 AN: 150870 Hom.: 905 Cov.: 31 AF XY: 0.0987 AC XY: 7277 AN XY: 73740

African (AFR) AF: 0.0782 AC: 3176 AN: 40626

American (AMR) AF: 0.116 AC: 1747 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3470

East Asian (EAS) AF: 0.103 AC: 533 AN: 5180

South Asian (SAS) AF: 0.0704 AC: 337 AN: 4788

European-Finnish (FIN) AF: 0.0526 AC: 557 AN: 10580

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.124 AC: 8443 AN: 67838

Other (OTH) AF: 0.115 AC: 241 AN: 2096

Alfa AF: 0.114 Hom.: 3523

Bravo AF: 0.108

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	10
DANN	Benign	0.67
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2524050; hg19: chr6-31255541;