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. Variant got 2 ACMG points: 2P and 0B. PM2

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. 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

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.610-65_610-3dupTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_acceptor_variant, intron_variant	Intron 2 of 13	ENST00000616016.5	NP_001372570.1
SAMD11	NM_001385640.1	c.610-65_610-3dupTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_acceptor_variant, intron_variant	Intron 2 of 13		NP_001372569.1
SAMD11	NM_152486.4	c.73-65_73-3dupTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACC		splice_acceptor_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.610-74_610-73insGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCTGCCCCACCTTCCTCTCCTCCT		intron_variant	Intron 2 of 13	5	NM_001385641.1	ENSP00000478421.2

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

Gnomad4 AFR AF: 0.0000243

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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

LitVar

Other links and lift over

dbSNP: rs879326979; hg19: chr1-865461;