chr11-102798678-T-C

Variant names:

• chr11-102798678-T-C
• rs1144393
• ENST00000371455.7:n.423+556T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000525739.6(WTAPP1):​n.682+556T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,960 control chromosomes in the GnomAD database, including 7,205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.29 (7205 hom., cov: 31)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.45
• Publications: 37 publications found

Genes affected

WTAPP1 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 11-102798678-T-C is Benign according to our data. Variant chr11-102798678-T-C is described in ClinVar as Benign. ClinVar VariationId is 1229767.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 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+556T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.423+556T>C		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.682+556T>C		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.443+556T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44667 AN: 151842 Hom.: 7202 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.294 AC: 44669 AN: 151960 Hom.: 7205 Cov.: 31 AF XY: 0.286 AC XY: 21214 AN XY: 74268

African (AFR) AF: 0.196 AC: 8119 AN: 41460

American (AMR) AF: 0.247 AC: 3775 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3468

East Asian (EAS) AF: 0.0869 AC: 448 AN: 5156

South Asian (SAS) AF: 0.172 AC: 828 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3041 AN: 10560

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26335 AN: 67918

Other (OTH) AF: 0.304 AC: 642 AN: 2110

Alfa AF: 0.347 Hom.: 14338

Bravo AF: 0.286

Asia WGS AF: 0.108 AC: 379 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.52
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1144393; hg19: chr11-102669409;