15-66733879-C-T

Position:

• chr15-66733879-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005585.5(SMAD6):​c.952+17381C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,116 control chromosomes in the GnomAD database, including 38,681 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 0.71 (38681 hom., cov: 32)
• Consequence: SMAD6 NM_005585.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

Genes affected

SMAD6 (HGNC:6772): (SMAD family member 6) The protein encoded by this gene belongs to the SMAD family of proteins, which are related to Drosophila 'mothers against decapentaplegic' (Mad) and C. elegans Sma. SMAD proteins are signal transducers and transcriptional modulators that mediate multiple signaling pathways. This protein functions in the negative regulation of BMP and TGF-beta/activin-signalling. Multiple transcript variants have been found for this gene.[provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMAD6	NM_005585.5	c.952+17381C>T		intron_variant		ENST00000288840.10	NP_005576.3
SMAD6	XM_011521561.3	c.169+17381C>T		intron_variant			XP_011519863.1
SMAD6	NR_027654.2	n.2107+16739C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMAD6	ENST00000288840.10	c.952+17381C>T		intron_variant		1	NM_005585.5	ENSP00000288840	P1
SMAD6	ENST00000557916.5	c.*67+16739C>T		intron_variant, NMD_transcript_variant		1		ENSP00000452955
SMAD6	ENST00000559931.5	c.*67+16739C>T		intron_variant, NMD_transcript_variant		3		ENSP00000453446

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108367 AN: 151998 Hom.: 38655 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.713 AC: 108440 AN: 152116 Hom.: 38681 Cov.: 32 AF XY: 0.717 AC XY: 53307 AN XY: 74340

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.730

Alfa AF: 0.709 Hom.: 20334

Bravo AF: 0.715

Asia WGS AF: 0.768 AC: 2672 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	1.8
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2053423; hg19: chr15-67026217;