chr4-145463623-G-T

Variant names:

• chr4-145463623-G-T
• rs1866179
• ENST00000658284.2:n.530+4856C>A

Variant summary

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

The ENST00000658284.2(SMAD1-AS2):​n.530+4856C>A 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 152,004 control chromosomes in the GnomAD database, including 8,967 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 (8967 hom., cov: 31)
• Consequence: SMAD1-AS2 ENST00000658284.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 3 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=-0.93).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAD1-AS2	ENST00000658284.2		n.530+4856C>A		intron	N/A
	SMAD1-AS2	ENST00000813541.1		n.496+4856C>A		intron	N/A
	SMAD1-AS2	ENST00000813542.1		n.454+4856C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46074 AN: 151886 Hom.: 8965 Cov.: 31

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0984

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.303 AC: 46073 AN: 152004 Hom.: 8967 Cov.: 31 AF XY: 0.300 AC XY: 22288 AN XY: 74262

African (AFR) AF: 0.0776 AC: 3224 AN: 41522

American (AMR) AF: 0.247 AC: 3768 AN: 15262

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

East Asian (EAS) AF: 0.0976 AC: 506 AN: 5182

South Asian (SAS) AF: 0.293 AC: 1406 AN: 4798

European-Finnish (FIN) AF: 0.457 AC: 4809 AN: 10532

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

European-Non Finnish (NFE) AF: 0.444 AC: 30191 AN: 67924

Other (OTH) AF: 0.303 AC: 639 AN: 2108

Alfa AF: 0.378 Hom.: 9238

Bravo AF: 0.275

Asia WGS AF: 0.178 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.23
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1866179; hg19: chr4-146384775;