rs11167682

Variant names:

• chr5-154442782-G-T
• rs11167682
• ENST00000524264.6:n.195+580C>A

Variant summary

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

The ENST00000524264.6(SAP30L-AS1):​n.195+580C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,896 control chromosomes in the GnomAD database, including 6,205 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 (6205 hom., cov: 32)
• Consequence: SAP30L-AS1 ENST00000524264.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 9 publications found

Genes affected

SAP30L-AS1 (HGNC:26760): (SAP30L antisense RNA 1 (head to head))

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524264.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAP30L-AS1	NR_037897.1		n.204+580C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAP30L-AS1	ENST00000524264.6	TSL:1	n.195+580C>A		intron	N/A
	SAP30L-AS1	ENST00000501280.4	TSL:5	n.232+580C>A		intron	N/A
	SAP30L-AS1	ENST00000519727.5	TSL:3	n.201+580C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41768 AN: 151778 Hom.: 6184 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.275 AC: 41835 AN: 151896 Hom.: 6205 Cov.: 32 AF XY: 0.273 AC XY: 20234 AN XY: 74246

African (AFR) AF: 0.370 AC: 15337 AN: 41398

American (AMR) AF: 0.198 AC: 3021 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2271 AN: 5154

South Asian (SAS) AF: 0.157 AC: 754 AN: 4816

European-Finnish (FIN) AF: 0.256 AC: 2693 AN: 10524

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16007 AN: 67948

Other (OTH) AF: 0.260 AC: 548 AN: 2108

Alfa AF: 0.248 Hom.: 7798

Bravo AF: 0.277

Asia WGS AF: 0.289 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.3
DANN	Benign	0.63
PhyloP100		0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11167682;

hg19: chr5-153822342;