NM_001385641.1:c.610-23_610-3dupTTCCTCTCCTCCTGCCCCACC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001385641.1(SAMD11):​c.610-23_610-3dupTTCCTCTCCTCCTGCCCCACC variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000445 in 1,475,002 control chromosomes in the GnomAD database, including 16 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00047 ( 16 hom. )

Consequence

SAMD11
NM_001385641.1 splice_acceptor, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.291
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000473 (626/1323458) while in subpopulation EAS AF= 0.0169 (589/34838). AF 95% confidence interval is 0.0158. There are 16 homozygotes in gnomad4_exome. There are 320 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 16 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SAMD11NM_001385641.1 linkc.610-23_610-3dupTTCCTCTCCTCCTGCCCCACC splice_acceptor_variant, intron_variant Intron 2 of 13 ENST00000616016.5 NP_001372570.1
SAMD11NM_001385640.1 linkc.610-23_610-3dupTTCCTCTCCTCCTGCCCCACC splice_acceptor_variant, intron_variant Intron 2 of 13 NP_001372569.1
SAMD11NM_152486.4 linkc.73-23_73-3dupTTCCTCTCCTCCTGCCCCACC splice_acceptor_variant, intron_variant Intron 2 of 13 NP_689699.3 Q96NU1-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SAMD11ENST00000616016.5 linkc.610-74_610-73insGCCCCACCTTCCTCTCCTCCT intron_variant Intron 2 of 13 5 NM_001385641.1 ENSP00000478421.2 A0A087WU74

Frequencies

GnomAD3 genomes
AF:
0.000198
AC:
30
AN:
151426
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000194
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000657
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00330
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000590
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000473
AC:
626
AN:
1323458
Hom.:
16
AF XY:
0.000494
AC XY:
320
AN XY:
647992
show subpopulations
Gnomad4 AFR exome
AF:
0.0000331
Gnomad4 AMR exome
AF:
0.0000618
Gnomad4 ASJ exome
AF:
0.0000462
Gnomad4 EAS exome
AF:
0.0169
Gnomad4 SAS exome
AF:
0.000144
Gnomad4 FIN exome
AF:
0.0000218
Gnomad4 NFE exome
AF:
0.0000146
Gnomad4 OTH exome
AF:
0.000127
GnomAD4 genome
AF:
0.000198
AC:
30
AN:
151544
Hom.:
0
Cov.:
33
AF XY:
0.000162
AC XY:
12
AN XY:
74028
show subpopulations
Gnomad4 AFR
AF:
0.000194
Gnomad4 AMR
AF:
0.0000656
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00331
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000590
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs879326979; hg19: chr1-865461; API