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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+13650A>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+13650A>C		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+13650A>C		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+13650A>C		intron_variant	Intron 2 of 3	4
WTAPP1	ENST00000817290.1	n.287+13650A>C		intron_variant	Intron 3 of 4

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 v4.3

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

Publications

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Other links and lift over

dbSNP: rs502174; hg19: chr11-102682503;