6-31288976-T-G

Variant names:

• chr6-31288976-T-G
• rs2524044

Variant summary

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

The variant allele was found at a frequency of 0.156 in 152,712 control chromosomes in the GnomAD database, including 2,057 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 0.16 (2042 hom., cov: 32)
  • Exomes 𝑓: 0.22 (15 hom.)
• Consequence: WASF5P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 29 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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
	ENSG00000298396	ENST00000755297.1		n.32+17870T>G		intron	N/A
	WASF5P	ENST00000428639.1	TSL:6	n.-12A>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23657 AN: 152040 Hom.: 2041 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.165

GnomAD4 exome AF: 0.219 AC: 121 AN: 552 Hom.: 15 Cov.: 0 AF XY: 0.182 AC XY: 56 AN XY: 308

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.200 AC: 2 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 2 AN: 18

East Asian (EAS) AF: 0.167 AC: 1 AN: 6

South Asian (SAS) AF: 0.364 AC: 16 AN: 44

European-Finnish (FIN) AF: 0.323 AC: 20 AN: 62

Middle Eastern (MID) AF: 0.207 AC: 12 AN: 58

European-Non Finnish (NFE) AF: 0.189 AC: 61 AN: 322

Other (OTH) AF: 0.214 AC: 6 AN: 28

GnomAD4 genome AF: 0.156 AC: 23661 AN: 152160 Hom.: 2042 Cov.: 32 AF XY: 0.154 AC XY: 11447 AN XY: 74386

African (AFR) AF: 0.106 AC: 4397 AN: 41516

American (AMR) AF: 0.235 AC: 3598 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.182 AC: 942 AN: 5174

South Asian (SAS) AF: 0.194 AC: 934 AN: 4824

European-Finnish (FIN) AF: 0.117 AC: 1242 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11387 AN: 67978

Other (OTH) AF: 0.164 AC: 348 AN: 2116

Alfa AF: 0.164 Hom.: 8568

Bravo AF: 0.163

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2524044; hg19: chr6-31256753;