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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Links

KCNQ1 (HGNC:6294):

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
KCNQ1	NM_000218.3 linkuse as main transcript	c.1795-29246C>T		intron_variant		ENST00000155840.12
KCNQ1	NM_181798.1 linkuse as main transcript	c.1414-29246C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNQ1	ENST00000155840.12 linkuse as main transcript	c.1795-29246C>T		intron_variant		1	NM_000218.3	P1	P51787-1

Frequencies

GnomAD3 genomes

AF:

0.0958

AC:

14571

AN:

152038

Hom.:

1182

Cov.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over