12-69667006-G-T

Variant names:

• chr12-69667006-G-T
• rs7310083
• NM_032735.3:c.1100+4422C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032735.3(BEST3):​c.1100+4422C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,104 control chromosomes in the GnomAD database, including 1,256 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 0.11 (1256 hom., cov: 32)
• Consequence: BEST3 NM_032735.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

Genes affected

BEST3 (HGNC:17105): (bestrophin 3) BEST3 belongs to the bestrophin family of anion channels, which includes BEST1 (MIM 607854), the gene mutant in vitelliform macular dystrophy (VMD; MIM 153700), and 2 other BEST1-like genes, BEST2 (MIM 607335) and BEST4 (MIM 607336). Bestrophins are transmembrane (TM) proteins that share a homology region containing a high content of aromatic residues, including an invariant arg-phe-pro (RFP) motif. The bestrophin genes share a conserved gene structure, with almost identical sizes of the 8 RFP-TM domain-encoding exons and highly conserved exon-intron boundaries. Each of the 4 bestrophin genes has a unique 3-prime end of variable length (Stohr et al., 2002 [PubMed 12032738]; Tsunenari et al., 2003 [PubMed 12907679]).[supplied by OMIM, Mar 2008]

LOC105369823 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BEST3	NM_032735.3	c.1100+4422C>A		intron_variant	Intron 9 of 9	ENST00000330891.10	NP_116124.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BEST3	ENST00000330891.10	c.1100+4422C>A		intron_variant	Intron 9 of 9	5	NM_032735.3	ENSP00000332413.5

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16101 AN: 151986 Hom.: 1255 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0244

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0558

Gnomad OTH AF: 0.133

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.106 AC: 16129 AN: 152104 Hom.: 1256 Cov.: 32 AF XY: 0.104 AC XY: 7759 AN XY: 74358

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0904

Gnomad4 EAS AF: 0.0530

Gnomad4 SAS AF: 0.0724

Gnomad4 FIN AF: 0.0244

Gnomad4 NFE AF: 0.0558

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0672 Hom.: 676

Bravo AF: 0.118

Asia WGS AF: 0.0740 AC: 261 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.54
DANN	Benign	0.45

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

LitVar

Other links and lift over

dbSNP: rs7310083; hg19: chr12-70060786;