rs17208967

Variant names:

• chr15-66933256-T-C
• rs17208967
• ENST00000558436.2:n.432-1432A>G

Variant summary

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

The ENST00000558436.2(SMASR):​n.432-1432A>G variant causes a intron 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 ENST00000558436.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558436.2. 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
	SMASR	NR_135687.1		n.429-1432A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMASR	ENST00000558436.2	TSL:3	n.432-1432A>G		intron	N/A
	SMASR	ENST00000733462.1		n.277-1432A>G		intron	N/A

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

African (AFR) AF: 0.135 AC: 5585 AN: 41502

American (AMR) AF: 0.154 AC: 2354 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5180

South Asian (SAS) AF: 0.0845 AC: 408 AN: 4828

European-Finnish (FIN) AF: 0.186 AC: 1968 AN: 10586

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14614 AN: 67968

Other (OTH) AF: 0.175 AC: 369 AN: 2112

Alfa AF: 0.193 Hom.: 1331

Bravo AF: 0.170

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.60
PhyloP100		-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17208967;

hg19: chr15-67225594;