5-32584479-G-C

Variant names:

• chr5-32584479-G-C
• rs2008245
• ENST00000506237.6:c.-1-4033G>C

Variant summary

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

The ENST00000506237.6(SUB1):​c.-1-4033G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 143,318 control chromosomes in the GnomAD database, including 8,814 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 0.35 (8814 hom., cov: 28)
• Consequence: SUB1 ENST00000506237.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 2 publications found

Genes affected

SUB1 (HGNC:19985): (SUB1 regulator of transcription) Enables identical protein binding activity; single-stranded DNA binding activity; and transcription coactivator activity. Involved in negative regulation of DNA metabolic process and regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of transcription regulator complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506237.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUB1	ENST00000506237.6	TSL:2	c.-1-4033G>C		intron	N/A	ENSP00000422078.1
	SUB1	ENST00000512913.5	TSL:2	c.-1-4033G>C		intron	N/A	ENSP00000422806.1
	SUB1	ENST00000513013.5	TSL:5	n.211-7084G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.346 AC: 49494 AN: 143240 Hom.: 8813 Cov.: 28

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.345 AC: 49501 AN: 143318 Hom.: 8814 Cov.: 28 AF XY: 0.350 AC XY: 24286 AN XY: 69396

African (AFR) AF: 0.195 AC: 7297 AN: 37478

American (AMR) AF: 0.390 AC: 5445 AN: 13970

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1200 AN: 3406

East Asian (EAS) AF: 0.385 AC: 1838 AN: 4776

South Asian (SAS) AF: 0.426 AC: 1961 AN: 4600

European-Finnish (FIN) AF: 0.468 AC: 4362 AN: 9330

Middle Eastern (MID) AF: 0.303 AC: 86 AN: 284

European-Non Finnish (NFE) AF: 0.394 AC: 26234 AN: 66574

Other (OTH) AF: 0.340 AC: 683 AN: 2010

Alfa AF: 0.246 Hom.: 682

Bravo AF: 0.314

Asia WGS AF: 0.360 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.098
DANN	Benign	0.39
PhyloP100		-0.77
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: rs2008245; hg19: chr5-32584585;