rs1729659

Positions:

• chr2-61077136-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001129993.3(SANBR):​c.648A>G​(p.Lys216Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 1,606,506 control chromosomes in the GnomAD database, including 85,568 homozygotes. 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: 𝑓 0.33 (8913 hom., cov: 32)
  • Exomes 𝑓: 0.32 (76655 hom.)
• Consequence: SANBR NM_001129993.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399

Genes affected

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

SANBR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP7: Synonymous conserved (PhyloP=0.399 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SANBR	NM_001129993.3	c.648A>G	p.Lys216Lys	synonymous_variant	6/22	ENST00000402291.6	NP_001123465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SANBR	ENST00000402291.6	c.648A>G	p.Lys216Lys	synonymous_variant	6/22	1	NM_001129993.3	ENSP00000385579.1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50844 AN: 151940 Hom.: 8890 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.362

GnomAD3 exomes AF: 0.329 AC: 82114 AN: 249920 Hom.: 14162 AF XY: 0.321 AC XY: 43395 AN XY: 135044

Gnomad AFR exome AF: 0.382

Gnomad AMR exome AF: 0.404

Gnomad ASJ exome AF: 0.382

Gnomad EAS exome AF: 0.435

Gnomad SAS exome AF: 0.223

Gnomad FIN exome AF: 0.227

Gnomad NFE exome AF: 0.323

Gnomad OTH exome AF: 0.336

GnomAD4 exome AF: 0.320 AC: 466034 AN: 1454448 Hom.: 76655 Cov.: 30 AF XY: 0.317 AC XY: 229437 AN XY: 723828

Gnomad4 AFR exome AF: 0.382

Gnomad4 AMR exome AF: 0.402

Gnomad4 ASJ exome AF: 0.384

Gnomad4 EAS exome AF: 0.434

Gnomad4 SAS exome AF: 0.225

Gnomad4 FIN exome AF: 0.225

Gnomad4 NFE exome AF: 0.321

Gnomad4 OTH exome AF: 0.331

GnomAD4 genome AF: 0.335 AC: 50919 AN: 152058 Hom.: 8913 Cov.: 32 AF XY: 0.330 AC XY: 24517 AN XY: 74346

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.361

Alfa AF: 0.329 Hom.: 14297

Bravo AF: 0.356

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.4
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1729659; hg19: chr2-61304271; COSMIC: COSV54373736; COSMIC: COSV54373736;