dbSNP rs2242471: SDAD1:p.Ser575Cys (chr4-75957563-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018115.4(SDAD1):c.1724C>G(p.Ser575Cys) variant causes a missense change. The variant allele was found at a frequency of 0.377 in 1,613,754 control chromosomes in the GnomAD database, including 120,091 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.33 ( 9184 hom., cov: 32)

Exomes 𝑓: 0.38 ( 110907 hom. )

Consequence

SDAD1
NM_018115.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.09

Variant links:

Genes affected

SDAD1 (HGNC:25537): (SDA1 domain containing 1) Predicted to be involved in ribosomal large subunit biogenesis and ribosomal large subunit export from nucleus. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SDAD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003446132).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDAD1	NM_018115.4 link	c.1724C>G	p.Ser575Cys	missense_variant	Exon 19 of 22	ENST00000356260.10	NP_060585.2	Q9NVU7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDAD1	ENST00000356260.10 link	c.1724C>G	p.Ser575Cys	missense_variant	Exon 19 of 22	1	NM_018115.4	ENSP00000348596.5		Q9NVU7-1

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

50333

AN:

151932

Hom.:

9191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.253

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.0688

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.397

Gnomad OTH

AF:

0.319

GnomAD3 exomes

AF:

0.335

AC:

84202

AN:

251444

Hom.:

16170

AF XY:

0.350

AC XY:

47532

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.244

Gnomad AMR exome

AF:

0.152

Gnomad ASJ exome

AF:

0.360

Gnomad EAS exome

AF:

0.0580

Gnomad SAS exome

AF:

0.448

Gnomad FIN exome

AF:

0.440

Gnomad NFE exome

AF:

0.396

Gnomad OTH exome

AF:

0.334

GnomAD4 exome

AF:

0.382

AC:

557868

AN:

1461704

Hom.:

110907

Cov.:

AF XY:

0.384

AC XY:

279112

AN XY:

727162

show subpopulations

Gnomad4 AFR exome

AF:

0.247

Gnomad4 AMR exome

AF:

0.162

Gnomad4 ASJ exome

AF:

0.359

Gnomad4 EAS exome

AF:

0.0698

Gnomad4 SAS exome

AF:

0.443

Gnomad4 FIN exome

AF:

0.444

Gnomad4 NFE exome

AF:

0.400

Gnomad4 OTH exome

AF:

0.361

GnomAD4 genome

AF:

0.331

AC:

50326

AN:

152050

Hom.:

9184

Cov.:

AF XY:

0.331

AC XY:

24606

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.252

Gnomad4 AMR

AF:

0.231

Gnomad4 ASJ

AF:

0.365

Gnomad4 EAS

AF:

0.0688

Gnomad4 SAS

AF:

0.425

Gnomad4 FIN

AF:

0.452

Gnomad4 NFE

AF:

0.397

Gnomad4 OTH

AF:

0.320

Alfa

AF:

0.343

Hom.:

2877

Bravo

AF:

0.304

TwinsUK

AF:

0.389

AC:

1441

ALSPAC

AF:

0.392

AC:

1512

ESP6500AA

AF:

0.251

AC:

1104

ESP6500EA

AF:

0.391

AC:

3365

ExAC

AF:

0.341

AC:

41396

Asia WGS

AF:

0.270

AC:

942

AN:

3478

EpiCase

AF:

0.393

EpiControl

AF:

0.387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.088

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.35

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.013

T;.

Eigen

Uncertain

0.42

Eigen_PC

Uncertain

0.48

FATHMM_MKL

Uncertain

0.93

LIST_S2

Uncertain

0.91

D;D

MetaRNN

Benign

0.0034

T;T

MetaSVM

Benign

-1.2

MutationAssessor

Uncertain

2.1

M;.

PrimateAI

Benign

0.43

PROVEAN

Benign

-1.7

N;N

REVEL

Benign

0.18

Sift

Benign

0.047

D;T

Sift4G

Uncertain

0.060

T;T

Polyphen

0.60

P;P

Vest4

0.069

MPC

0.19

ClinPred

0.025

GERP RS

5.2

Varity_R

0.49

gMVP

0.14

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