11-2709955-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000218.3(KCNQ1):c.1514+47874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,094 control chromosomes in the GnomAD database, including 1,255 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 0.12 (1255 hom., cov: 32)
• Consequence: KCNQ1 NM_000218.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNQ1	NM_000218.3	c.1514+47874C>T		intron_variant		ENST00000155840.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNQ1	ENST00000155840.12	c.1514+47874C>T		intron_variant		1	NM_000218.3	P1
KCNQ1	ENST00000335475.6	c.1133+47874C>T		intron_variant		1
KCNQ1	ENST00000496887.7	c.1157+47874C>T		intron_variant		5
KCNQ1	ENST00000646564.2	c.974+47874C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18715 AN: 151976 Hom.: 1244 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.0676

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.123 AC: 18760 AN: 152094 Hom.: 1255 Cov.: 32 AF XY: 0.127 AC XY: 9473 AN XY: 74324

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.0855

Gnomad4 EAS AF: 0.0673

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0788 Hom.: 152

Bravo AF: 0.108

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
Dann	Benign	0.66

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

Other links and lift over

dbSNP: rs231901; hg19: chr11-2731185;