Variant chr12-31984918-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_018169.4(RESF1):c.3963C>G(p.Thr1321=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,611,740 control chromosomes in the GnomAD database, including 30,582 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 0.17 ( 2426 hom., cov: 32)

Exomes 𝑓: 0.19 ( 28156 hom. )

Consequence

RESF1
NM_018169.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.333

Variant links:

Genes affected

RESF1 (HGNC:25559): (retroelement silencing factor 1) Predicted to enable histone binding activity and histone methyltransferase binding activity. Predicted to be involved in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate and positive regulation of DNA methylation-dependent heterochromatin assembly. Predicted to act upstream of or within response to bacterium. Predicted to be located in nucleus. Predicted to colocalize with gamma-tubulin complex. [provided by Alliance of Genome Resources, Apr 2022]

RESF1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP7

Synonymous conserved (PhyloP=-0.333 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RESF1	NM_018169.4 linkuse as main transcript	c.3963C>G	p.Thr1321=	synonymous_variant	4/6	ENST00000312561.9	NP_060639.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
RESF1	ENST00000312561.9 linkuse as main transcript	c.3963C>G	p.Thr1321=	synonymous_variant	4/6	1	NM_018169.4	ENSP00000310338	P1
RESF1	ENST00000397578.7 linkuse as main transcript	n.139-2321C>G		intron_variant, non_coding_transcript_variant		3
RESF1	ENST00000535596.5 linkuse as main transcript	n.318-2321C>G		intron_variant, non_coding_transcript_variant		2
RESF1	ENST00000541981.5 linkuse as main transcript	n.218-7460C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25838

AN:

151918

Hom.:

2428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.0903

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.260

Gnomad NFE

AF:

0.199

Gnomad OTH

AF:

0.174

GnomAD3 exomes

AF:

0.176

AC:

43852

AN:

249044

Hom.:

4189

AF XY:

0.184

AC XY:

24725

AN XY:

134464

show subpopulations

Gnomad AFR exome

AF:

0.112

Gnomad AMR exome

AF:

0.103

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.0794

Gnomad SAS exome

AF:

0.233

Gnomad FIN exome

AF:

0.200

Gnomad NFE exome

AF:

0.199

Gnomad OTH exome

AF:

0.200

GnomAD4 exome

AF:

0.193

AC:

282159

AN:

1459704

Hom.:

28156

Cov.:

AF XY:

0.196

AC XY:

141939

AN XY:

725926

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.110

Gnomad4 ASJ exome

AF:

0.222

Gnomad4 EAS exome

AF:

0.120

Gnomad4 SAS exome

AF:

0.235

Gnomad4 FIN exome

AF:

0.195

Gnomad4 NFE exome

AF:

0.197

Gnomad4 OTH exome

AF:

0.193

GnomAD4 genome

AF:

0.170

AC:

25835

AN:

152036

Hom.:

2426

Cov.:

AF XY:

0.170

AC XY:

12629

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.116

Gnomad4 AMR

AF:

0.148

Gnomad4 ASJ

AF:

0.232

Gnomad4 EAS

AF:

0.0903

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.199

Gnomad4 OTH

AF:

0.172

Alfa

AF:

0.191

Hom.:

937

Bravo

AF:

0.162

Asia WGS

AF:

0.139

AC:

483

AN:

3476

EpiCase

AF:

0.196

EpiControl

AF:

0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.27

DANN

Benign

0.42

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