rs820218

Variant names:

• chr17-75691415-G-A
• rs820218
• ENST00000578288.5:n.395G>A

Variant summary

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

The ENST00000578288.5(SAP30BP):​n.395G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 456,364 control chromosomes in the GnomAD database, including 19,853 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 0.28 (6159 hom., cov: 32)
  • Exomes 𝑓: 0.29 (13694 hom.)
• Consequence: SAP30BP ENST00000578288.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 21 publications found

Genes affected

SAP30BP (HGNC:30785): (SAP30 binding protein) Involved in modulation by host of symbiont transcription; positive regulation of histone deacetylation; and response to virus. Located in intermediate filament cytoskeleton and nucleoplasm. [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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAP30BP	NM_013260.8	c.265-2025G>A		intron_variant	Intron 3 of 10	ENST00000584667.6	NP_037392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAP30BP	ENST00000584667.6	c.265-2025G>A		intron_variant	Intron 3 of 10	1	NM_013260.8	ENSP00000462116.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42060 AN: 151874 Hom.: 6157 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.285

GnomAD2 exomes AF: 0.271 AC: 36454 AN: 134420 AF XY: 0.273

Gnomad AFR exome AF: 0.207

Gnomad AMR exome AF: 0.188

Gnomad ASJ exome AF: 0.418

Gnomad EAS exome AF: 0.156

Gnomad FIN exome AF: 0.312

Gnomad NFE exome AF: 0.335

Gnomad OTH exome AF: 0.318

GnomAD4 exome AF: 0.289 AC: 87988 AN: 304372 Hom.: 13694 Cov.: 0 AF XY: 0.285 AC XY: 49393 AN XY: 173326

African (AFR) AF: 0.213 AC: 1835 AN: 8626

American (AMR) AF: 0.188 AC: 5139 AN: 27276

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 4476 AN: 10788

East Asian (EAS) AF: 0.151 AC: 1394 AN: 9210

South Asian (SAS) AF: 0.214 AC: 12766 AN: 59734

European-Finnish (FIN) AF: 0.305 AC: 3900 AN: 12794

Middle Eastern (MID) AF: 0.408 AC: 1136 AN: 2782

European-Non Finnish (NFE) AF: 0.333 AC: 52866 AN: 158928

Other (OTH) AF: 0.314 AC: 4476 AN: 14234

GnomAD4 genome AF: 0.277 AC: 42077 AN: 151992 Hom.: 6159 Cov.: 32 AF XY: 0.272 AC XY: 20184 AN XY: 74308

African (AFR) AF: 0.216 AC: 8940 AN: 41470

American (AMR) AF: 0.226 AC: 3454 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3472

East Asian (EAS) AF: 0.156 AC: 810 AN: 5180

South Asian (SAS) AF: 0.190 AC: 916 AN: 4812

European-Finnish (FIN) AF: 0.302 AC: 3190 AN: 10552

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22475 AN: 67930

Other (OTH) AF: 0.282 AC: 596 AN: 2114

Alfa AF: 0.317 Hom.: 14499

Bravo AF: 0.273

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.5
DANN	Benign	0.81
PhyloP100		-0.25
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs820218; hg19: chr17-73687495; COSMIC: COSV53128046; COSMIC: COSV53128046;