chr11-102764770-T-C

Variant names:

• chr11-102764770-T-C
• rs10791595
• ENST00000371455.7:n.324+13344T>C

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.324+13344T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,064 control chromosomes in the GnomAD database, including 9,995 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 0.36 (9995 hom., cov: 32)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 14 publications found

Genes affected

WTAPP1 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371455.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.324+13344T>C		intron	N/A
	WTAPP1	ENST00000817290.1		n.188+13344T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54643 AN: 151946 Hom.: 9976 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.360 AC: 54695 AN: 152064 Hom.: 9995 Cov.: 32 AF XY: 0.358 AC XY: 26620 AN XY: 74348

African (AFR) AF: 0.334 AC: 13839 AN: 41476

American (AMR) AF: 0.364 AC: 5557 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3468

East Asian (EAS) AF: 0.587 AC: 3029 AN: 5160

South Asian (SAS) AF: 0.415 AC: 1999 AN: 4822

European-Finnish (FIN) AF: 0.281 AC: 2976 AN: 10574

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25031 AN: 67964

Other (OTH) AF: 0.362 AC: 765 AN: 2116

Alfa AF: 0.364 Hom.: 20791

Bravo AF: 0.363

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs10791595; hg19: chr11-102635501;