rs1144396

Variant names:

• chr11-102808321-C-A
• rs1144396

Your query was ambiguous. Multiple possible variants found:

• chr11-102808321-C-A
• chr11-102808321-C-G

Variant summary

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

The variant allele was found at a frequency of 0.469 in 152,058 control chromosomes in the GnomAD database, including 17,086 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 0.47 (17086 hom., cov: 33)
• Consequence: CSNK1A1P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 12 publications found

Genes affected

CSNK1A1P2 (HGNC:30445):

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	NR_038390.1		n.682+10199C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.423+10199C>A		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.682+10199C>A		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.443+10199C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71202 AN: 151940 Hom.: 17059 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.469 AC: 71270 AN: 152058 Hom.: 17086 Cov.: 33 AF XY: 0.459 AC XY: 34137 AN XY: 74334

African (AFR) AF: 0.517 AC: 21454 AN: 41468

American (AMR) AF: 0.381 AC: 5819 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3468

East Asian (EAS) AF: 0.328 AC: 1694 AN: 5160

South Asian (SAS) AF: 0.289 AC: 1393 AN: 4824

European-Finnish (FIN) AF: 0.383 AC: 4047 AN: 10566

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33985 AN: 67968

Other (OTH) AF: 0.477 AC: 1007 AN: 2110

Alfa AF: 0.461 Hom.: 7639

Bravo AF: 0.471

Asia WGS AF: 0.357 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.85
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1144396; hg19: chr11-102679052;