11-102785475-T-C

Position:

• chr11-102785475-T-C

Variant summary

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

The NR_038390.1(WTAPP1):​n.389+1411T>C 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 0.949 in 152,314 control chromosomes in the GnomAD database, including 68,643 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 0.95 (68643 hom., cov: 33)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WTAPP1	NR_038390.1	n.389+1411T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.325-12549T>C		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.389+1411T>C		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.344+1411T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144383 AN: 152196 Hom.: 68585 Cov.: 33

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.949 AC: 144500 AN: 152314 Hom.: 68643 Cov.: 33 AF XY: 0.945 AC XY: 70377 AN XY: 74456

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.939

Alfa AF: 0.925 Hom.: 5922

Bravo AF: 0.948

Asia WGS AF: 0.910 AC: 3166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs470226; hg19: chr11-102656206; COSMIC: COSV54247520;