Menu
GeneBe

rs2237895

chr11-2835964-A-Cchr11-2835964-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000218.3(KCNQ1):c.1795-11803A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151480 control chromosomes in the gnomAD Genomes database, including 10273 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 0.35 ( 10273 hom., cov: 30)

Consequence

KCNQ1
NM_000218.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.04

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KCNQ1NM_000218.3 linkuse as main transcriptc.1795-11803A>C intron_variant ENST00000155840.12
KCNQ1NM_181798.1 linkuse as main transcriptc.1414-11803A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCNQ1ENST00000155840.12 linkuse as main transcriptc.1795-11803A>C intron_variant 1 NM_000218.3 P1P51787-1

Frequencies

GnomAD3 genomes
AF:
0.352
AC:
53270
AN:
151480
Hom.:
10273
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.184
Gnomad AMI
AF:
0.501
Gnomad AMR
AF:
0.381
Gnomad ASJ
AF:
0.448
Gnomad EAS
AF:
0.335
Gnomad SAS
AF:
0.393
Gnomad FIN
AF:
0.496
Gnomad MID
AF:
0.370
Gnomad NFE
AF:
0.415
Gnomad OTH
AF:
0.370
Alfa
AF:
0.397
Hom.:
16166
Bravo
AF:
0.340
Asia WGS
AF:
0.331
AC:
1155
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
Cadd
Benign
0.60
Dann
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2237895; hg19: chr11-2857194;