9-104031445-A-G

Variant names:

• chr9-104031445-A-G
• rs1536895
• ENST00000773568.1:n.241+11928T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000773568.1(SMC2-DT):​n.241+11928T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0947 in 152,244 control chromosomes in the GnomAD database, including 719 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 0.095 (719 hom., cov: 32)
• Consequence: SMC2-DT ENST00000773568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 4 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 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.241+11928T>C		intron_variant	Intron 2 of 2
SMC2-DT	ENST00000773569.1	n.930+11928T>C		intron_variant	Intron 6 of 6
SMC2-DT	ENST00000773570.1	n.275+11928T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14407 AN: 152126 Hom.: 721 Cov.: 32

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0947 AC: 14415 AN: 152244 Hom.: 719 Cov.: 32 AF XY: 0.0977 AC XY: 7275 AN XY: 74438

African (AFR) AF: 0.0924 AC: 3835 AN: 41522

American (AMR) AF: 0.0932 AC: 1426 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3470

East Asian (EAS) AF: 0.121 AC: 629 AN: 5188

South Asian (SAS) AF: 0.0811 AC: 391 AN: 4822

European-Finnish (FIN) AF: 0.150 AC: 1588 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0876 AC: 5956 AN: 68022

Other (OTH) AF: 0.103 AC: 218 AN: 2114

Alfa AF: 0.0898 Hom.: 580

Bravo AF: 0.0902

Asia WGS AF: 0.123 AC: 428 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	16
DANN	Benign	0.79
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1536895; hg19: chr9-106793726;