rs7726475

Variant names:

• chr5-32575808-G-A
• rs7726475
• ENST00000506237.5:c.-1-12704G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-32575808-G-A
• chr5-32575808-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506237.5(SUB1):​c.-1-12704G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,158 control chromosomes in the GnomAD database, including 5,679 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 0.24 (5679 hom., cov: 33)
• Consequence: SUB1 ENST00000506237.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUB1	ENST00000506237.5	c.-1-12704G>A		intron_variant	Intron 1 of 4	2		ENSP00000422078.1
SUB1	ENST00000512913.5	c.-2+4634G>A		intron_variant	Intron 2 of 5	2		ENSP00000422806.1
SUB1	ENST00000513013.5	n.210+4634G>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37254 AN: 152040 Hom.: 5676 Cov.: 33

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.245 AC: 37248 AN: 152158 Hom.: 5679 Cov.: 33 AF XY: 0.246 AC XY: 18313 AN XY: 74376

Gnomad4 AFR AF: 0.0684

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.265

Alfa AF: 0.241 Hom.: 1494

Bravo AF: 0.229

Asia WGS AF: 0.198 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.60

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

Other links and lift over

dbSNP: rs7726475; hg19: chr5-32575914;