rs1044880

Variant names:

• chr19-16880222-C-G
• rs1044880
• NM_001297595.2:c.*1495C>G

Your query was ambiguous. Multiple possible variants found:

• chr19-16880222-C-G
• chr19-16880222-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001297595.2(SIN3B):​c.*1495C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SIN3B NM_001297595.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 1 publications found

Genes affected

SIN3B (HGNC:19354): (SIN3 transcription regulator family member B) Predicted to enable transcription corepressor activity. Predicted to be involved in histone deacetylation; negative regulation of transcription by RNA polymerase II; and striated muscle tissue development. Predicted to be located in nucleus. Predicted to be part of Sin3 complex. Predicted to be active in chromatin. [provided by Alliance of Genome Resources, Apr 2022]

SIN3B Gene-Disease associations (from GenCC):

• SIN3A-related intellectual disability syndrome due to a point mutation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• syndromic intellectual disability

  Inheritance: AD Classification: LIMITED Submitted by: G2P

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIN3B	NM_001297595.2	c.*1495C>G		3_prime_UTR_variant	Exon 19 of 19	ENST00000248054.10	NP_001284524.1
SIN3B	NM_015260.4	c.*1495C>G		3_prime_UTR_variant	Exon 20 of 20		NP_056075.1
SIN3B	NM_001297597.2	c.*1495C>G		3_prime_UTR_variant	Exon 10 of 10		NP_001284526.1
SIN3B	XM_006722704.2	c.*1495C>G		3_prime_UTR_variant	Exon 11 of 11		XP_006722767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIN3B	ENST00000248054.10	c.*1495C>G		3_prime_UTR_variant	Exon 19 of 19	1	NM_001297595.2	ENSP00000248054.4
SIN3B	ENST00000379803.5	c.*1495C>G		3_prime_UTR_variant	Exon 20 of 20	1		ENSP00000369131.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.77
PhyloP100		1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1044880; hg19: chr19-16991033;