rs17797449

Variant names:

• chr4-145447634-T-C
• rs17797449
• ENST00000658284.2:n.531-2198A>G

Variant summary

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

The ENST00000658284.2(SMAD1-AS2):​n.531-2198A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 150,960 control chromosomes in the GnomAD database, including 9,068 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 0.31 (9068 hom., cov: 32)
• Consequence: SMAD1-AS2 ENST00000658284.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.935
• Publications: 2 publications found

Genes affected

SMAD1-AS2 (HGNC:49381): (SMAD1 antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658284.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAD1-AS2	ENST00000658284.2		n.531-2198A>G		intron	N/A
	SMAD1-AS2	ENST00000813541.1		n.496+20845A>G		intron	N/A
	SMAD1-AS2	ENST00000813542.1		n.454+20845A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47178 AN: 150842 Hom.: 9066 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.313 AC: 47179 AN: 150960 Hom.: 9068 Cov.: 32 AF XY: 0.309 AC XY: 22811 AN XY: 73740

African (AFR) AF: 0.106 AC: 4280 AN: 40514

American (AMR) AF: 0.250 AC: 3810 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1053 AN: 3466

East Asian (EAS) AF: 0.0985 AC: 509 AN: 5166

South Asian (SAS) AF: 0.297 AC: 1415 AN: 4766

European-Finnish (FIN) AF: 0.457 AC: 4819 AN: 10548

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30165 AN: 67968

Other (OTH) AF: 0.308 AC: 648 AN: 2102

Alfa AF: 0.367 Hom.: 1513

Bravo AF: 0.283

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.4
DANN	Benign	0.81
PhyloP100		0.94

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: rs17797449;

hg19: chr4-146368786;