chr4-145473163-T-A

Variant names:

• chr4-145473163-T-A
• rs11724777
• ENST00000658284.2:n.194-3442A>T

Variant summary

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

The ENST00000658284.2(SMAD1-AS2):​n.194-3442A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,202 control chromosomes in the GnomAD database, including 9,004 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 0.30 (9004 hom., cov: 32)
• Consequence: SMAD1-AS2 ENST00000658284.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAD1-AS2	ENST00000658284.2		n.194-3442A>T		intron	N/A
	SMAD1-AS2	ENST00000813541.1		n.160-3442A>T		intron	N/A
	SMAD1-AS2	ENST00000813542.1		n.118-3442A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46173 AN: 152084 Hom.: 9002 Cov.: 32

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.303 AC: 46172 AN: 152202 Hom.: 9004 Cov.: 32 AF XY: 0.300 AC XY: 22336 AN XY: 74404

African (AFR) AF: 0.0776 AC: 3226 AN: 41558

American (AMR) AF: 0.247 AC: 3774 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1053 AN: 3472

East Asian (EAS) AF: 0.0981 AC: 508 AN: 5178

South Asian (SAS) AF: 0.295 AC: 1424 AN: 4826

European-Finnish (FIN) AF: 0.456 AC: 4832 AN: 10600

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30238 AN: 67970

Other (OTH) AF: 0.302 AC: 638 AN: 2110

Alfa AF: 0.372 Hom.: 1491

Bravo AF: 0.276

Asia WGS AF: 0.179 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.57
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11724777; hg19: chr4-146394315;