rs2408490

Positions:

• chr11-102801822-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038390.1(WTAPP1):​n.682+3700C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,032 control chromosomes in the GnomAD database, including 3,379 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 0.20 (3379 hom., cov: 32)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94

Genes affected

WTAPP1 (HGNC:44115): (WTAP pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WTAPP1	NR_038390.1	n.682+3700C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+3700C>T		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.682+3700C>T		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.443+3700C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30891 AN: 151914 Hom.: 3360 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.204 AC: 30961 AN: 152032 Hom.: 3379 Cov.: 32 AF XY: 0.201 AC XY: 14958 AN XY: 74298

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.191

Alfa AF: 0.176 Hom.: 3473

Bravo AF: 0.204

Asia WGS AF: 0.243 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.083
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2408490; hg19: chr11-102672553;