11-102802182-T-C

Variant names:

• chr11-102802182-T-C
• rs470307
• ENST00000371455.7:n.423+4060T>C

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.423+4060T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.973 in 152,308 control chromosomes in the GnomAD database, including 72,220 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 0.97 (72220 hom., cov: 33)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 1 publications found

Genes affected

WTAPP1 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+4060T>C		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+4060T>C		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+4060T>C		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+4060T>C		intron_variant	Intron 2 of 3	4
WTAPP1	ENST00000817290.1	n.287+4060T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.973 AC: 148075 AN: 152190 Hom.: 72162 Cov.: 33

Gnomad AFR AF: 0.996

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.971

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

GnomAD4 genome AF: 0.973 AC: 148191 AN: 152308 Hom.: 72220 Cov.: 33 AF XY: 0.967 AC XY: 72017 AN XY: 74462

African (AFR) AF: 0.996 AC: 41398 AN: 41576

American (AMR) AF: 0.901 AC: 13771 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.982 AC: 3409 AN: 3472

East Asian (EAS) AF: 0.889 AC: 4612 AN: 5190

South Asian (SAS) AF: 0.967 AC: 4667 AN: 4828

European-Finnish (FIN) AF: 0.918 AC: 9722 AN: 10594

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67360 AN: 68040

Other (OTH) AF: 0.971 AC: 2049 AN: 2110

Alfa AF: 0.983 Hom.: 9142

Bravo AF: 0.971

Asia WGS AF: 0.944 AC: 3282 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	0.77
DANN	Benign	0.27
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs470307; hg19: chr11-102672913;