chr9-104010478-A-G

Variant names:

• chr9-104010478-A-G
• rs1867347
• ENST00000773568.1:n.242-31821T>C

Variant summary

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

The ENST00000773568.1(SMC2-DT):​n.242-31821T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,962 control chromosomes in the GnomAD database, including 20,849 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 0.52 (20849 hom., cov: 32)
• Consequence: SMC2-DT ENST00000773568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 1 publications found

Genes affected

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

LINC03094 (HGNC:56725): (long intergenic non-protein coding RNA 3094)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 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
SMC2-DT	ENST00000773568.1	n.242-31821T>C		intron_variant	Intron 2 of 2
SMC2-DT	ENST00000773569.1	n.931-31821T>C		intron_variant	Intron 6 of 6
SMC2-DT	ENST00000773570.1	n.276-10207T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78281 AN: 151844 Hom.: 20822 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.516 AC: 78366 AN: 151962 Hom.: 20849 Cov.: 32 AF XY: 0.518 AC XY: 38445 AN XY: 74268

African (AFR) AF: 0.600 AC: 24876 AN: 41486

American (AMR) AF: 0.526 AC: 8029 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1450 AN: 3468

East Asian (EAS) AF: 0.796 AC: 4084 AN: 5128

South Asian (SAS) AF: 0.539 AC: 2596 AN: 4814

European-Finnish (FIN) AF: 0.463 AC: 4886 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 30984 AN: 67936

Other (OTH) AF: 0.514 AC: 1083 AN: 2108

Alfa AF: 0.476 Hom.: 57045

Bravo AF: 0.525

Asia WGS AF: 0.644 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.80
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1867347; hg19: chr9-106772759;