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rs2237892

Variant summary

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

The NM_000218.3(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 0.096 in 152,156 control chromosomes in the GnomAD database, including 1,189 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 ( 1189 hom., cov: 32)

Consequence

KCNQ1
NM_000218.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03
Variant links:
Genes affected
KCNQ1 (HGNC:6294): (potassium voltage-gated channel subfamily Q member 1) This gene encodes a voltage-gated potassium channel required for repolarization phase of the cardiac action potential. This protein can form heteromultimers with two other potassium channel proteins, KCNE1 and KCNE3. Mutations in this gene are associated with hereditary long QT syndrome 1 (also known as Romano-Ward syndrome), Jervell and Lange-Nielsen syndrome, and familial atrial fibrillation. This gene exhibits tissue-specific imprinting, with preferential expression from the maternal allele in some tissues, and biallelic expression in others. This gene is located in a region of chromosome 11 amongst other imprinted genes that are associated with Beckwith-Wiedemann syndrome (BWS), and itself has been shown to be disrupted by chromosomal rearrangements in patients with BWS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2011]

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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
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 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

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
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0960
AC:
14612
AN:
152156
Hom.:
1189
Cov.:
32
AF XY:
0.0975
AC XY:
7254
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.219
Gnomad4 ASJ
AF:
0.0568
Gnomad4 EAS
AF:
0.344
Gnomad4 SAS
AF:
0.0292
Gnomad4 FIN
AF:
0.0556
Gnomad4 NFE
AF:
0.0613
Gnomad4 OTH
AF:
0.0866
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
1.8
Dann
Benign
0.40

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: rs2237892; hg19: chr11-2839751; API