chr17-17824629-T-A

Variant names:

• chr17-17824629-T-A
• rs9899634
• NM_004176.5:c.92-4108A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004176.5(SREBF1):​c.92-4108A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,972 control chromosomes in the GnomAD database, including 21,402 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 0.51 (21402 hom., cov: 32)
• Consequence: SREBF1 NM_004176.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• Publications: 25 publications found

Genes affected

SREBF1 (HGNC:11289): (sterol regulatory element binding transcription factor 1) This gene encodes a basic helix-loop-helix-leucine zipper (bHLH-Zip) transcription factor that binds to the sterol regulatory element-1 (SRE1), which is a motif that is found in the promoter of the low density lipoprotein receptor gene and other genes involved in sterol biosynthesis. The encoded protein is synthesized as a precursor that is initially attached to the nuclear membrane and endoplasmic reticulum. Following cleavage, the mature protein translocates to the nucleus and activates transcription. This cleaveage is inhibited by sterols. This gene is located within the Smith-Magenis syndrome region on chromosome 17. Alternative promoter usage and splicing result in multiple transcript variants, including SREBP-1a and SREBP-1c, which correspond to RefSeq transcript variants 2 and 3, respectively. [provided by RefSeq, Nov 2017]

SREBF1 Gene-Disease associations (from GenCC):

• hereditary mucoepithelial dysplasia

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: G2P, PanelApp Australia
• IFAP syndrome 2

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
• Hirschsprung disease

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SREBF1	NM_004176.5	c.92-4108A>T		intron_variant	Intron 1 of 18	ENST00000261646.11	NP_004167.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SREBF1	ENST00000261646.11	c.92-4108A>T		intron_variant	Intron 1 of 18	1	NM_004176.5	ENSP00000261646.5
SREBF1	ENST00000355815.8	c.92-1022A>T		intron_variant	Intron 1 of 19	1		ENSP00000348069.4
SREBF1	ENST00000395757.6	c.92-4108A>T		intron_variant	Intron 1 of 18	2		ENSP00000379106.2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77855 AN: 151854 Hom.: 21380 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.0813

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.530

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.513 AC: 77928 AN: 151972 Hom.: 21402 Cov.: 32 AF XY: 0.502 AC XY: 37316 AN XY: 74290

African (AFR) AF: 0.402 AC: 16639 AN: 41420

American (AMR) AF: 0.449 AC: 6864 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1982 AN: 3466

East Asian (EAS) AF: 0.0813 AC: 421 AN: 5176

South Asian (SAS) AF: 0.280 AC: 1347 AN: 4804

European-Finnish (FIN) AF: 0.565 AC: 5961 AN: 10556

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42930 AN: 67952

Other (OTH) AF: 0.529 AC: 1119 AN: 2114

Alfa AF: 0.437 Hom.: 1274

Bravo AF: 0.501

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.74
PhyloP100		0.58
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9899634; hg19: chr17-17727943;