Variant rs4074794 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001135054.2(SIGIRR):c.7+53C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,363,522 control chromosomes in the GnomAD database, including 28,365 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 0.22 ( 4125 hom., cov: 34)

Exomes 𝑓: 0.18 ( 24240 hom. )

Consequence

SIGIRR
NM_001135054.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.887

Variant links:

Genes affected

SIGIRR (HGNC:30575): (single Ig and TIR domain containing) Predicted to enable NAD+ nucleosidase activity. Involved in negative regulation of DNA-binding transcription factor activity. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

SIGIRR links:

SIGIRR (HGNC:):

SIGIRR 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=-0.63).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIGIRR	NM_001135054.2 linkuse as main transcript	c.7+53C>T		intron_variant		ENST00000431843.7	NP_001128526.1	Q6IA17-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIGIRR	ENST00000431843.7 linkuse as main transcript	c.7+53C>T		intron_variant		1	NM_001135054.2	ENSP00000403104.2		Q6IA17-1

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32892

AN:

152072

Hom.:

4134

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.580

Gnomad SAS

AF:

0.357

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.222

GnomAD4 exome

AF:

0.181

AC:

219182

AN:

1211332

Hom.:

24240

Cov.:

AF XY:

0.183

AC XY:

107318

AN XY:

587952

show subpopulations

Gnomad4 AFR exome

AF:

0.261

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.168

Gnomad4 EAS exome

AF:

0.648

Gnomad4 SAS exome

AF:

0.299

Gnomad4 FIN exome

AF:

0.138

Gnomad4 NFE exome

AF:

0.160

Gnomad4 OTH exome

AF:

0.211

GnomAD4 genome

AF:

0.216

AC:

32903

AN:

152190

Hom.:

4125

Cov.:

AF XY:

0.220

AC XY:

16372

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.263

Gnomad4 AMR

AF:

0.231

Gnomad4 ASJ

AF:

0.174

Gnomad4 EAS

AF:

0.579

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.134

Gnomad4 NFE

AF:

0.162

Gnomad4 OTH

AF:

0.221

Alfa

AF:

0.185

Hom.:

1460

Bravo

AF:

0.224

Asia WGS

AF:

0.454

AC:

1578

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

DANN

Benign

0.76

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