rs7107224

Variant names:

• chr11-102801775-A-C
• rs7107224
• ENST00000371455.7:n.423+3653A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-102801775-A-C
• chr11-102801775-A-T

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.682+3653A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,142 control chromosomes in the GnomAD database, including 3,390 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 0.20 (3390 hom., cov: 32)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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+3653A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.423+3653A>C		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.682+3653A>C		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.443+3653A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30904 AN: 152024 Hom.: 3371 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.204 AC: 30974 AN: 152142 Hom.: 3390 Cov.: 32 AF XY: 0.201 AC XY: 14963 AN XY: 74390

African (AFR) AF: 0.289 AC: 12000 AN: 41472

American (AMR) AF: 0.140 AC: 2134 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1120 AN: 5176

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4818

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10594

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11407 AN: 68010

Other (OTH) AF: 0.191 AC: 403 AN: 2112

Alfa AF: 0.101 Hom.: 147

Bravo AF: 0.204

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.6
DANN	Benign	0.75
PhyloP100		1.2

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: rs7107224;

hg19: chr11-102672506;