2-61070492-C-T

Variant names:

• chr2-61070492-C-T
• rs1002948247
• NM_001129993.3:c.142C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001129993.3(SANBR):​c.142C>T​(p.Pro48Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P48T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SANBR NM_001129993.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.16
• Publications: 0 publications found

Genes affected

SANBR (HGNC:29387): (SANT and BTB domain regulator of CSR)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11262292).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001129993.3. 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
	SANBR	NM_001129993.3	MANE Select	c.142C>T	p.Pro48Ser	missense	Exon 3 of 22	NP_001123465.1	Q6NSI8-1
	SANBR	NM_001330436.2		c.142C>T	p.Pro48Ser	missense	Exon 3 of 22	NP_001317365.1	Q6NSI8-1
	SANBR	NM_001330433.2		c.142C>T	p.Pro48Ser	missense	Exon 3 of 22	NP_001317362.1	Q6NSI8-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SANBR	ENST00000402291.6	TSL:1 MANE Select	c.142C>T	p.Pro48Ser	missense	Exon 3 of 22	ENSP00000385579.1	Q6NSI8-1
	SANBR	ENST00000295031.9	TSL:1	c.142C>T	p.Pro48Ser	missense	Exon 3 of 22	ENSP00000295031.5	Q6NSI8-2
	SANBR	ENST00000453186.5	TSL:1	n.142C>T		non_coding_transcript_exon	Exon 3 of 21	ENSP00000413200.1	F8VWD7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1453462 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 722918

African (AFR) AF: 0.00 AC: 0 AN: 33042

American (AMR) AF: 0.00 AC: 0 AN: 42820

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26026

East Asian (EAS) AF: 0.00 AC: 0 AN: 38986

South Asian (SAS) AF: 0.00 AC: 0 AN: 84354

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53324

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5754

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1109108

Other (OTH) AF: 0.00 AC: 0 AN: 60048

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.051	T
Eigen	Benign	-0.075
Eigen_PC	Benign	0.16
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.88	D
M_CAP	Benign	0.0057	T
MetaRNN	Benign	0.11	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.27	N
PhyloP100		4.2
PrimateAI	Benign	0.46	T
PROVEAN	Uncertain	-2.4	N
REVEL	Benign	0.087
Sift	Benign	0.24	T
Sift4G	Benign	0.46	T
Polyphen		0.049	B
Vest4		0.15
MutPred		0.27		Loss of phosphorylation at T47 (P = 0.0848)
MVP		0.47
MPC		0.082
ClinPred		0.84	D
GERP RS		5.0
PromoterAI		-0.025	Neutral
Varity_R		0.11
gMVP		0.41
Mutation Taster		=76/24	polymorphism

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: rs1002948247; hg19: chr2-61297627;