rs879326979

Variant names:

• chr1-930081-AGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT-A
• 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. Variant got 2 ACMG points: 2P and 0B. PM2

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. 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

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD11	NM_001385641.1	c.610-44_610-3delTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_region_variant, intron_variant	Intron 2 of 13	ENST00000616016.5	NP_001372570.1
SAMD11	NM_001385640.1	c.610-44_610-3delTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_region_variant, intron_variant	Intron 2 of 13		NP_001372569.1
SAMD11	NM_152486.4	c.73-44_73-3delTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_region_variant, intron_variant	Intron 2 of 13		NP_689699.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD11	ENST00000616016.5	c.610-73_610-32delGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT		intron_variant	Intron 2 of 13	5	NM_001385641.1	ENSP00000478421.2

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000309

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000435

Gnomad4 NFE exome AF: 0.00000679

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-865461;