rs879326979

Variant names:

• chr1-930081-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT-A
• rs879326979
• NM_001385641.1:c.610-44_610-3delTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC

Your query was ambiguous. Multiple possible variants found:

• chr1-930081-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT-A
• chr1-930081-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT-AGCCCCACCTTCCTCTCCTCCT
• chr1-930081-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT
• chr1-930081-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT

Variant summary

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

The NM_001385641.1(SAMD11):​c.610-44_610-3delTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000756 in 1,323,490 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 DEL_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: not found (cov: 33)
  • Exomes 𝑓: 0.0000076 (0 hom.)
• Consequence: SAMD11 NM_001385641.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• 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.610-44_610-3delTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_region intron	N/A	NP_001372570.1	A0A087WU74
	SAMD11	NM_001385640.1		c.610-44_610-3delTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_region intron	N/A	NP_001372569.1	A0A087WX24
	SAMD11	NM_152486.4		c.73-44_73-3delTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_region 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.610-73_610-32delGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT		intron	N/A	ENSP00000478421.2	A0A087WU74
	SAMD11	ENST00000968543.1		c.610-73_610-32delGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT		intron	N/A	ENSP00000638602.1
	SAMD11	ENST00000618323.5	TSL:5	c.610-73_610-32delGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT		intron	N/A	ENSP00000480678.2	A0A087WX24

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000756 AC: 10 AN: 1323490 Hom.: 0 AF XY: 0.00000772 AC XY: 5 AN XY: 648006

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 30198

American (AMR) AF: 0.0000309 AC: 1 AN: 32360

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21666

East Asian (EAS) AF: 0.00 AC: 0 AN: 34866

South Asian (SAS) AF: 0.00 AC: 0 AN: 69430

European-Finnish (FIN) AF: 0.0000435 AC: 2 AN: 45972

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3876

European-Non Finnish (NFE) AF: 0.00000679 AC: 7 AN: 1030190

Other (OTH) AF: 0.00 AC: 0 AN: 54932

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000146490), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3

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;