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GeneBe

rs2237892

Variant summary

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

The NM_000218(KCNQ1):c.1795-29246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 152038 control chromosomes in the gnomAD Genomes database, including 1182 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 0.096 ( 1182 hom., cov: 32)

Consequence

KCNQ1
NM_000218 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KCNQ1NM_000218.3 linkuse as main transcriptc.1795-29246C>T intron_variant ENST00000155840.12
KCNQ1NM_181798.1 linkuse as main transcriptc.1414-29246C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCNQ1ENST00000155840.12 linkuse as main transcriptc.1795-29246C>T intron_variant 1 NM_000218.3 P1P51787-1

Frequencies

GnomAD3 genomes
AF:
0.0958
AC:
14571
AN:
152038
Hom.:
1182
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.100
Gnomad AMI
AF:
0.0263
Gnomad AMR
AF:
0.218
Gnomad ASJ
AF:
0.0568
Gnomad EAS
AF:
0.344
Gnomad SAS
AF:
0.0290
Gnomad FIN
AF:
0.0556
Gnomad MID
AF:
0.0570
Gnomad NFE
AF:
0.0613
Gnomad OTH
AF:
0.0822
Alfa
AF:
0.0739
Hom.:
1567
Bravo
AF:
0.111
Asia WGS
AF:
0.198
AC:
685
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
0.46
Dann
Benign
0.40

Splicing

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: rs2237892; hg19: chr11-2839751;