Variant 2-85343265-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_017750.4(RETSAT):c.1810C>A(p.Arg604=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00289 in 1,611,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0039 ( 0 hom., cov: 36)

Exomes 𝑓: 0.0028 ( 0 hom. )

Consequence

RETSAT
NM_017750.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.36

Variant links:

Genes affected

RETSAT (HGNC:25991): (retinol saturase) Predicted to enable all-trans-retinol 13,14-reductase activity. Predicted to be involved in retinol metabolic process. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

RETSAT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 2-85343265-G-T is Benign according to our data. Variant chr2-85343265-G-T is described in ClinVar as [Benign]. Clinvar id is 771334.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.36 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RETSAT	NM_017750.4 linkuse as main transcript	c.1810C>A	p.Arg604=	synonymous_variant	11/11	ENST00000295802.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RETSAT	ENST00000295802.9 linkuse as main transcript	c.1810C>A	p.Arg604=	synonymous_variant	11/11	1	NM_017750.4	P1	Q6NUM9-1
RETSAT	ENST00000429806.5 linkuse as main transcript	c.*197C>A		3_prime_UTR_variant, NMD_transcript_variant	8/8	1
RETSAT	ENST00000449375.1 linkuse as main transcript	c.1177C>A	p.Arg393=	synonymous_variant	8/8	5
RETSAT	ENST00000438611.4 linkuse as main transcript	c.*785C>A		3_prime_UTR_variant, NMD_transcript_variant	6/6	5

Frequencies

GnomAD3 genomes

AF:

0.00394

AC:

599

AN:

152060

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0139

Gnomad ASJ

AF:

0.00432

Gnomad EAS

AF:

0.0629

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000206

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00808

AC:

2017

AN:

249554

Hom.:

AF XY:

0.00672

AC XY:

907

AN XY:

135044

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.0304

Gnomad ASJ exome

AF:

0.00129

Gnomad EAS exome

AF:

0.0496

Gnomad SAS exome

AF:

0.000752

Gnomad FIN exome

AF:

0.00213

Gnomad NFE exome

AF:

0.000176

Gnomad OTH exome

AF:

0.00409

GnomAD4 exome

AF:

0.00278

AC:

4064

AN:

1459662

Hom.:

Cov.:

AF XY:

0.00263

AC XY:

1910

AN XY:

726270

show subpopulations

Gnomad4 AFR exome

AF:

0.000179

Gnomad4 AMR exome

AF:

0.0308

Gnomad4 ASJ exome

AF:

0.00165

Gnomad4 EAS exome

AF:

0.0581

Gnomad4 SAS exome

AF:

0.00107

Gnomad4 FIN exome

AF:

0.00118

Gnomad4 NFE exome

AF:

0.0000818

Gnomad4 OTH exome

AF:

0.00302

GnomAD4 genome

AF:

0.00395

AC:

601

AN:

152178

Hom.:

Cov.:

AF XY:

0.00425

AC XY:

316

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.000192

Gnomad4 AMR

AF:

0.0139

Gnomad4 ASJ

AF:

0.00432

Gnomad4 EAS

AF:

0.0636

Gnomad4 SAS

AF:

0.000827

Gnomad4 FIN

AF:

0.00188

Gnomad4 NFE

AF:

0.000206

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.000411

Hom.:

EpiCase

AF:

0.000109

EpiControl

AF:

0.000119

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.5

DANN

Benign

0.36

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