rs10037670

Variant names:

• chr5-154431930-A-G
• rs10037670
• ENST00000524264.6:n.195+11432T>C

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+11432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,164 control chromosomes in the GnomAD database, including 3,398 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 0.21 (3398 hom., cov: 33)
• Consequence: SAP30L-AS1 ENST00000524264.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAP30L-AS1	NR_037897.1	n.204+11432T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAP30L-AS1	ENST00000524264.6	n.195+11432T>C		intron_variant	Intron 2 of 2	1
SAP30L-AS1	ENST00000519727.5	n.201+11432T>C		intron_variant	Intron 2 of 3	3
SAP30L-AS1	ENST00000652895.1	n.195+11432T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31735 AN: 152046 Hom.: 3404 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.209 AC: 31727 AN: 152164 Hom.: 3398 Cov.: 33 AF XY: 0.209 AC XY: 15534 AN XY: 74390

African (AFR) AF: 0.237 AC: 9851 AN: 41500

American (AMR) AF: 0.196 AC: 2995 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 685 AN: 3468

East Asian (EAS) AF: 0.105 AC: 543 AN: 5188

South Asian (SAS) AF: 0.244 AC: 1175 AN: 4824

European-Finnish (FIN) AF: 0.239 AC: 2530 AN: 10574

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13343 AN: 68002

Other (OTH) AF: 0.213 AC: 451 AN: 2116

Alfa AF: 0.197 Hom.: 5033

Bravo AF: 0.206

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.86
DANN	Benign	0.87
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs10037670; hg19: chr5-153811490;