1-930081-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT

Variant names:

• chr1-930081-A-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT
• rs879326979
• NM_001385641.1:c.610-65_610-3dupTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001385641.1(SAMD11):​c.610-65_610-3dupTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000066 in 151,428 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
• Consequence: SAMD11 NM_001385641.1 splice_acceptor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 0 publications found

Genes affected

SAMD11 (HGNC:28706): (sterile alpha motif domain containing 11) Predicted to enable several functions, including histone binding activity; protein domain specific binding activity; and protein self-association. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SAMD11 Gene-Disease associations (from GenCC):

• retinitis pigmentosa

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Franklin by Genoox

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385641.1. 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
	SAMD11	NM_001385641.1	MANE Select	c.610-65_610-3dupTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_acceptor intron	N/A	NP_001372570.1	A0A087WU74
	SAMD11	NM_001385640.1		c.610-65_610-3dupTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_acceptor intron	N/A	NP_001372569.1	A0A087WX24
	SAMD11	NM_152486.4		c.73-65_73-3dupTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_acceptor intron	N/A	NP_689699.3	Q96NU1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD11	ENST00000616016.5	TSL:5 MANE Select	c.610-74_610-73insGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT		intron	N/A	ENSP00000478421.2	A0A087WU74
	SAMD11	ENST00000968543.1		c.610-74_610-73insGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT		intron	N/A	ENSP00000638602.1
	SAMD11	ENST00000618323.5	TSL:5	c.610-74_610-73insGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT		intron	N/A	ENSP00000480678.2	A0A087WX24

Frequencies

GnomAD3 genomes AF: 0.00000660 AC: 1 AN: 151428 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000660 AC: 1 AN: 151428 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 73900

African (AFR) AF: 0.0000243 AC: 1 AN: 41154

American (AMR) AF: 0.00 AC: 0 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5144

South Asian (SAS) AF: 0.00 AC: 0 AN: 4770

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10564

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67814

Other (OTH) AF: 0.00 AC: 0 AN: 2078

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs879326979; hg19: chr1-865461;