rs1670273

chr15-99073491-C-A

Variant summary

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

The ENST00000559468.1(SYNM-AS1):n.266+27232G>T 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 0.195 in 152,124 control chromosomes in the GnomAD database, including 3,605 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 0.20 (3605 hom., cov: 33)
• Consequence: SYNM-AS1 ENST00000559468.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

Genes affected

SYNM-AS1 (HGNC:55421): (SYNM antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYNM-AS1	XR_001751810.2	n.214-3795G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYNM-AS1	ENST00000559468.1	n.266+27232G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29677 AN: 152006 Hom.: 3588 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0455

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.195 AC: 29735 AN: 152124 Hom.: 3605 Cov.: 33 AF XY: 0.193 AC XY: 14376 AN XY: 74366

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0454

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.175

Alfa AF: 0.151 Hom.: 1362

Bravo AF: 0.201

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1670273; hg19: chr15-99616720;