chr4-145448604-T-C

Variant names:

• chr4-145448604-T-C
• rs13109195
• ENST00000658284.2:n.531-3168A>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.531-3168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0788 in 152,114 control chromosomes in the GnomAD database, including 536 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 0.079 (536 hom., cov: 31)
• Consequence: SMAD1-AS2 ENST00000658284.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMAD1-AS2	ENST00000658284.2	n.531-3168A>G		intron_variant	Intron 3 of 3
SMAD1-AS2	ENST00000813541.1	n.496+19875A>G		intron_variant	Intron 4 of 4
SMAD1-AS2	ENST00000813542.1	n.454+19875A>G		intron_variant	Intron 3 of 3
SMAD1-AS2	ENST00000813543.1	n.628-3168A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11974 AN: 151996 Hom.: 536 Cov.: 31

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0788 AC: 11980 AN: 152114 Hom.: 536 Cov.: 31 AF XY: 0.0796 AC XY: 5920 AN XY: 74346

African (AFR) AF: 0.0821 AC: 3407 AN: 41474

American (AMR) AF: 0.0896 AC: 1369 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3470

East Asian (EAS) AF: 0.0871 AC: 451 AN: 5176

South Asian (SAS) AF: 0.132 AC: 636 AN: 4808

European-Finnish (FIN) AF: 0.0663 AC: 702 AN: 10592

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0725 AC: 4927 AN: 68000

Other (OTH) AF: 0.0874 AC: 184 AN: 2106

Alfa AF: 0.0750 Hom.: 877

Bravo AF: 0.0779

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.76
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs13109195; hg19: chr4-146369756;