rs10512326

chr9-104092264-G-Achr9-104092264-G-C

Variant summary

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

The NR_121580.1(SMC2-DT):n.211C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,046 control chromosomes in the GnomAD database, including 8,086 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 (8086 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: SMC2-DT NR_121580.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

Genes affected

SMC2-DT (HGNC:50827): (SMC2 divergent transcript)

SMC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMC2-DT	NR_121580.1	n.211C>T		non_coding_transcript_exon_variant	1/3
SMC2	XM_011518149.4	c.-1750G>A		5_prime_UTR_variant	1/25
SMC2	XM_047422644.1	c.-1750G>A		5_prime_UTR_variant	1/24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMC2-DT	ENST00000603487.1	n.211C>T		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46492 AN: 151924 Hom.: 8087 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.329

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.306 AC: 46498 AN: 152042 Hom.: 8086 Cov.: 32 AF XY: 0.312 AC XY: 23173 AN XY: 74322

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.328

Alfa AF: 0.316 Hom.: 1333

Bravo AF: 0.317

Asia WGS AF: 0.554 AC: 1929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.4
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512326; hg19: chr9-106854545; COSMIC: COSV53956416;