rs470206

Positions:

• chr11-102800447-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.682+2325T>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 0.977 in 152,254 control chromosomes in the GnomAD database, including 72,748 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 0.98 (72748 hom., cov: 31)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

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 = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WTAPP1	NR_038390.1	n.682+2325T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+2325T>C		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.682+2325T>C		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.443+2325T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.977 AC: 148583 AN: 152136 Hom.: 72689 Cov.: 31

Gnomad AFR AF: 0.997

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.977 AC: 148699 AN: 152254 Hom.: 72748 Cov.: 31 AF XY: 0.970 AC XY: 72208 AN XY: 74412

Gnomad4 AFR AF: 0.997

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.982

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.974

Alfa AF: 0.979 Hom.: 30465

Bravo AF: 0.975

Asia WGS AF: 0.945 AC: 3284 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	0.39
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: rs470206; hg19: chr11-102671178;