rs10472812

Variant names:

• chr5-32592068-T-C
• rs10472812
• NM_006713.4:c.195+383T>C

Variant summary

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

The NM_006713.4(SUB1):​c.195+383T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,128 control chromosomes in the GnomAD database, including 8,823 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 0.33 (8823 hom., cov: 32)
• Consequence: SUB1 NM_006713.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUB1	NM_006713.4	c.195+383T>C		intron_variant	Intron 3 of 4	ENST00000265073.9	NP_006704.3
SUB1	XM_011513944.4	c.195+383T>C		intron_variant	Intron 4 of 5		XP_011512246.1
SUB1	XM_047416661.1	c.195+383T>C		intron_variant	Intron 4 of 5		XP_047272617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUB1	ENST00000265073.9	c.195+383T>C		intron_variant	Intron 3 of 4	1	NM_006713.4	ENSP00000265073.4

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49628 AN: 152010 Hom.: 8822 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.326 AC: 49636 AN: 152128 Hom.: 8823 Cov.: 32 AF XY: 0.328 AC XY: 24400 AN XY: 74360

African (AFR) AF: 0.176 AC: 7303 AN: 41524

American (AMR) AF: 0.359 AC: 5484 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1857 AN: 5180

South Asian (SAS) AF: 0.409 AC: 1977 AN: 4830

European-Finnish (FIN) AF: 0.418 AC: 4404 AN: 10548

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26280 AN: 67978

Other (OTH) AF: 0.323 AC: 682 AN: 2110

Alfa AF: 0.361 Hom.: 5466

Bravo AF: 0.313

Asia WGS AF: 0.362 AC: 1258 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	7.8
DANN	Benign	0.63
PhyloP100		0.24
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: rs10472812; hg19: chr5-32592174;