rs10512326

Variant names:

• chr9-104092264-G-A
• rs10512326
• XM_011518149.4:c.-1750G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-104092264-G-A
• chr9-104092264-G-C

Variant summary

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

The ENST00000603487.1(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 ENST00000603487.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 4 publications found

Genes affected

SMC2 (HGNC:14011): (structural maintenance of chromosomes 2) Predicted to enable ATP binding activity; chromatin binding activity; and single-stranded DNA binding activity. Involved in mitotic chromosome condensation. Located in condensed chromosome; cytoplasm; and nuclear lumen. Part of condensin complex. [provided by Alliance of Genome Resources, Apr 2022]

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000603487.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMC2-DT	NR_121580.1		n.211C>T		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMC2-DT	ENST00000603487.1	TSL:2	n.211C>T		non_coding_transcript_exon	Exon 1 of 3
	SMC2-DT	ENST00000773587.1		n.64C>T		non_coding_transcript_exon	Exon 1 of 2
	SMC2-DT	ENST00000603949.1	TSL:6	n.*138C>T		downstream_gene	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.222 AC: 9186 AN: 41470

American (AMR) AF: 0.428 AC: 6535 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1066 AN: 3468

East Asian (EAS) AF: 0.767 AC: 3958 AN: 5160

South Asian (SAS) AF: 0.423 AC: 2043 AN: 4826

European-Finnish (FIN) AF: 0.261 AC: 2760 AN: 10560

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20061 AN: 67962

Other (OTH) AF: 0.328 AC: 693 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.22
PhyloP100		-0.24

Splicing

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

Other links and lift over

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