rs603050

Variant names:

• chr11-102809498-C-T
• rs603050
• ENST00000371455.7:n.423+11376C>T

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.682+11376C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,044 control chromosomes in the GnomAD database, including 9,170 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 0.33 (9170 hom., cov: 33)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525739.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	NR_038390.1		n.682+11376C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.423+11376C>T		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.682+11376C>T		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.443+11376C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50833 AN: 151926 Hom.: 9147 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.335 AC: 50881 AN: 152044 Hom.: 9170 Cov.: 33 AF XY: 0.342 AC XY: 25396 AN XY: 74300

African (AFR) AF: 0.331 AC: 13717 AN: 41474

American (AMR) AF: 0.457 AC: 6979 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3470

East Asian (EAS) AF: 0.600 AC: 3106 AN: 5174

South Asian (SAS) AF: 0.565 AC: 2722 AN: 4816

European-Finnish (FIN) AF: 0.279 AC: 2949 AN: 10566

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19084 AN: 67952

Other (OTH) AF: 0.330 AC: 694 AN: 2106

Alfa AF: 0.324 Hom.: 1437

Bravo AF: 0.346

Asia WGS AF: 0.530 AC: 1841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.62
PhyloP100		0.38

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs603050;

hg19: chr11-102680229;