rs163171

Positions:

• chr11-2799835-T-C

Variant summary

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

The NM_000218.3(KCNQ1):​c.1794+21798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 152,062 control chromosomes in the GnomAD database, including 37,024 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 0.69 (37024 hom., cov: 32)
• Consequence: KCNQ1 NM_000218.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

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]

LOC124902614 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNQ1	NM_000218.3	c.1794+21798T>C		intron_variant		ENST00000155840.12	NP_000209.2
LOC124902614	XR_007062554.1	n.290A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNQ1	ENST00000155840.12	c.1794+21798T>C		intron_variant		1	NM_000218.3	ENSP00000155840	P1

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104164 AN: 151944 Hom.: 37026 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.685 AC: 104195 AN: 152062 Hom.: 37024 Cov.: 32 AF XY: 0.691 AC XY: 51389 AN XY: 74328

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.731

Alfa AF: 0.757 Hom.: 89916

Bravo AF: 0.664

Asia WGS AF: 0.725 AC: 2522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.39

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: rs163171; hg19: chr11-2821065; COSMIC: COSV50106394;