rs502174

Variant names:

• chr11-102811772-A-C
• rs502174
• ENST00000371455.7:n.423+13650A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-102811772-A-C
• chr11-102811772-A-G

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.682+13650A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,768 control chromosomes in the GnomAD database, including 15,313 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 0.44 (15313 hom., cov: 30)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 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+13650A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.423+13650A>C		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.682+13650A>C		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.443+13650A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67411 AN: 151650 Hom.: 15307 Cov.: 30

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.444 AC: 67442 AN: 151768 Hom.: 15313 Cov.: 30 AF XY: 0.435 AC XY: 32276 AN XY: 74168

African (AFR) AF: 0.431 AC: 17831 AN: 41338

American (AMR) AF: 0.375 AC: 5727 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1365 AN: 3466

East Asian (EAS) AF: 0.323 AC: 1665 AN: 5158

South Asian (SAS) AF: 0.286 AC: 1376 AN: 4806

European-Finnish (FIN) AF: 0.384 AC: 4032 AN: 10506

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33961 AN: 67910

Other (OTH) AF: 0.464 AC: 978 AN: 2110

Alfa AF: 0.443 Hom.: 6584

Bravo AF: 0.445

Asia WGS AF: 0.334 AC: 1162 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.50
DANN	Benign	0.54
PhyloP100		-1.1

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: rs502174;

hg19: chr11-102682503;