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rs2237895

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 0.351 in 151,598 control chromosomes in the GnomAD database, including 10,273 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
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=-0.94).
BA1
GnomAd4 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

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
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.351
AC:
53278
AN:
151598
Hom.:
10273
Cov.:
30
AF XY:
0.355
AC XY:
26291
AN XY:
74052
show subpopulations
Gnomad4 AFR
AF:
0.184
Gnomad4 AMR
AF:
0.381
Gnomad4 ASJ
AF:
0.448
Gnomad4 EAS
AF:
0.335
Gnomad4 SAS
AF:
0.394
Gnomad4 FIN
AF:
0.496
Gnomad4 NFE
AF:
0.415
Gnomad4 OTH
AF:
0.366
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
0.41
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; API