Variant chr1-108650337-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001102592.2(HENMT1):c.630C>T(p.Val210=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0037 in 1,613,964 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0029 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0038 ( 12 hom. )

Consequence

HENMT1
NM_001102592.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -6.42

Variant links:

Genes affected

HENMT1 (HGNC:26400): (HEN methyltransferase 1) Enables small RNA 2'-O-methyltransferase. Involved in RNA methylation. Predicted to be located in P granule. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

HENMT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 1-108650337-G-A is Benign according to our data. Variant chr1-108650337-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2638963.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-6.42 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
HENMT1	NM_001102592.2 linkuse as main transcript	c.630C>T	p.Val210=	synonymous_variant	7/8	ENST00000651461.1
HENMT1	NM_144584.3 linkuse as main transcript	c.630C>T	p.Val210=	synonymous_variant	7/8
HENMT1	XM_005270411.2 linkuse as main transcript	c.654C>T	p.Val218=	synonymous_variant	6/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HENMT1	ENST00000651461.1 linkuse as main transcript	c.630C>T	p.Val210=	synonymous_variant	7/8		NM_001102592.2	P1

Frequencies

GnomAD3 genomes

AF:

0.00295

AC:

448

AN:

152048

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000701

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00603

Gnomad ASJ

AF:

0.0138

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00390

Gnomad OTH

AF:

0.00383

GnomAD3 exomes

AF:

0.00314

AC:

790

AN:

251392

Hom.:

AF XY:

0.00337

AC XY:

458

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.000308

Gnomad AMR exome

AF:

0.00376

Gnomad ASJ exome

AF:

0.0150

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000719

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.00390

Gnomad OTH exome

AF:

0.00554

GnomAD4 exome

AF:

0.00378

AC:

5526

AN:

1461798

Hom.:

Cov.:

AF XY:

0.00370

AC XY:

2690

AN XY:

727204

show subpopulations

Gnomad4 AFR exome

AF:

0.000478

Gnomad4 AMR exome

AF:

0.00329

Gnomad4 ASJ exome

AF:

0.0147

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000939

Gnomad4 FIN exome

AF:

0.000150

Gnomad4 NFE exome

AF:

0.00414

Gnomad4 OTH exome

AF:

0.00414

GnomAD4 genome

AF:

0.00294

AC:

447

AN:

152166

Hom.:

Cov.:

AF XY:

0.00312

AC XY:

232

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.000699

Gnomad4 AMR

AF:

0.00602

Gnomad4 ASJ

AF:

0.0138

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.00390

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.00337

Hom.:

Bravo

AF:

0.00322

EpiCase

AF:

0.00464

EpiControl

AF:

0.00456

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2023

HENMT1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.48

DANN

Benign

0.61

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over