chr15-99073491-C-A

Variant names:

• chr15-99073491-C-A
• rs1670273
• ENST00000559468.1:n.266+27232G>T

Variant summary

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

The ENST00000559468.1(SYNM-AS1):​n.266+27232G>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559468.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYNM-AS1	ENST00000559468.1	TSL:4	n.266+27232G>T		intron	N/A

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

African (AFR) AF: 0.348 AC: 14415 AN: 41456

American (AMR) AF: 0.142 AC: 2177 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3472

East Asian (EAS) AF: 0.0454 AC: 235 AN: 5174

South Asian (SAS) AF: 0.134 AC: 646 AN: 4820

European-Finnish (FIN) AF: 0.146 AC: 1544 AN: 10600

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9263 AN: 68002

Other (OTH) AF: 0.175 AC: 370 AN: 2110

Alfa AF: 0.154 Hom.: 1838

Bravo AF: 0.201

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.9
DANN	Benign	0.78
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1670273; hg19: chr15-99616720;