2-61071661-A-C

Position:

• chr2-61071661-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001129993.3(SANBR):​c.206A>C​(p.Gln69Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000000695 in 1,438,124 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: SANBR NM_001129993.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.05

Genes affected

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

SANBR (HGNC:):

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/exons	MANE	Protein	UniProt
SANBR	NM_001129993.3	c.206A>C	p.Gln69Pro	missense_variant	4/22	ENST00000402291.6	NP_001123465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SANBR	ENST00000402291.6	c.206A>C	p.Gln69Pro	missense_variant	4/22	1	NM_001129993.3	ENSP00000385579.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.95e-7 AC: 1 AN: 1438124 Hom.: 0 Cov.: 30 AF XY: 0.00000140 AC XY: 1 AN XY: 714864

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000168

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 02, 2024

The c.206A>C (p.Q69P) alteration is located in exon 4 (coding exon 2) of the KIAA1841 gene. This alteration results from a A to C substitution at nucleotide position 206, causing the glutamine (Q) at amino acid position 69 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Uncertain	0.068	T
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.083	T;.;T;.
Eigen	Uncertain	0.39
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.88	.;.;D;D
M_CAP	Benign	0.0077	T
MetaRNN	Uncertain	0.64	D;D;D;D
MetaSVM	Benign	-0.81	T
MutationAssessor	Uncertain	2.2	M;M;M;M
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-1.7	N;N;N;N
REVEL	Benign	0.14
Sift	Uncertain	0.021	D;D;D;D
Sift4G	Uncertain	0.045	D;D;D;D
Polyphen		0.99	D;D;D;D
Vest4		0.79
MutPred		0.21		Loss of stability (P = 0.0629);Loss of stability (P = 0.0629);Loss of stability (P = 0.0629);Loss of stability (P = 0.0629);
MVP		0.67
MPC		0.10
ClinPred		0.89	D
GERP RS		4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.24
gMVP		0.68

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-61298796;