rs17208967

chr15-66933256-T-C

Variant summary

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

The NR_135687.1(SMASR):n.429-1432A>G 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 0.174 in 152,122 control chromosomes in the GnomAD database, including 2,581 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 0.17 (2581 hom., cov: 32)
• Consequence: SMASR NR_135687.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

SMASR (HGNC:53072): (SMAD3 associated long non-coding RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMASR	NR_135687.1	n.429-1432A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMASR	ENST00000558436.2	n.432-1432A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26487 AN: 152004 Hom.: 2585 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0846

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.174 AC: 26477 AN: 152122 Hom.: 2581 Cov.: 32 AF XY: 0.171 AC XY: 12748 AN XY: 74358

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0845

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.175

Alfa AF: 0.203 Hom.: 864

Bravo AF: 0.170

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.50
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17208967; hg19: chr15-67225594;