Variant rs981782 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021072.4(HCN1):c.1618+17983T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,870 control chromosomes in the GnomAD database, including 11,283 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 0.34 ( 11283 hom., cov: 32)

Consequence

HCN1
NM_021072.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.654

Variant links:

Genes affected

HCN1 (HGNC:4845): (hyperpolarization activated cyclic nucleotide gated potassium channel 1) The membrane protein encoded by this gene is a hyperpolarization-activated cation channel that contributes to the native pacemaker currents in heart and neurons. The encoded protein can homodimerize or heterodimerize with other pore-forming subunits to form a potassium channel. This channel may act as a receptor for sour tastes. [provided by RefSeq, Oct 2011]

HCN1 links:

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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=-0.56).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCN1	NM_021072.4 linkuse as main transcript	c.1618+17983T>G		intron_variant		ENST00000303230.6	NP_066550.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
HCN1	ENST00000303230.6 linkuse as main transcript	c.1618+17983T>G	intron_variant	1	NM_021072.4	ENSP00000307342	P2
HCN1	ENST00000673735.1 linkuse as main transcript	c.1618+17983T>G	intron_variant			ENSP00000501107	A2
HCN1	ENST00000637305.1 linkuse as main transcript	n.781+17983T>G	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.344

AC:

52268

AN:

151752

Hom.:

11285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0845

Gnomad AMI

AF:

0.569

Gnomad AMR

AF:

0.415

Gnomad ASJ

AF:

0.403

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.553

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.384

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

GnomAD4 genome

AF:

0.344

AC:

52266

AN:

151870

Hom.:

11283

Cov.:

AF XY:

0.344

AC XY:

25540

AN XY:

74172

show subpopulations

Gnomad4 AFR

AF:

0.0842

Gnomad4 AMR

AF:

0.415

Gnomad4 ASJ

AF:

0.403

Gnomad4 EAS

AF:

0.324

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.553

Gnomad4 NFE

AF:

0.460

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.423

Hom.:

13133

Bravo

AF:

0.328

Asia WGS

AF:

0.256

AC:

894

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.70

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over