17-47940435-T-G

Position:

• chr17-47940435-T-G

Variant summary

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

The NR_103857.1(SP2-AS1):​n.58+912A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,116 control chromosomes in the GnomAD database, including 19,886 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 0.50 (19886 hom., cov: 33)
• Consequence: SP2-AS1 NR_103857.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

Genes affected

SP2-AS1 (HGNC:51341): (SP2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SP2-AS1	NR_103857.1	n.58+912A>C		intron_variant, non_coding_transcript_variant
SP2-AS1	NR_103856.1	n.69+901A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SP2-AS1	ENST00000585280.5	n.54+901A>C		intron_variant, non_coding_transcript_variant		3
SP2-AS1	ENST00000411573.7	n.57+901A>C		intron_variant, non_coding_transcript_variant		2
SP2-AS1	ENST00000433001.1	n.44+912A>C		intron_variant, non_coding_transcript_variant		3
SP2-AS1	ENST00000451140.6	n.75+901A>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76572 AN: 151998 Hom.: 19838 Cov.: 33

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.504 AC: 76681 AN: 152116 Hom.: 19886 Cov.: 33 AF XY: 0.501 AC XY: 37288 AN XY: 74358

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.530

Alfa AF: 0.456 Hom.: 15890

Bravo AF: 0.509

Asia WGS AF: 0.618 AC: 2146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.70
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2325751; hg19: chr17-46017801;