16-69300977-C-CA

Position:

• chr16-69300977-C-CA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000336278.9(SNTB2):​c.*65dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 844,616 control chromosomes in the GnomAD database, including 2,559 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.16 (1803 hom., cov: 29)
  • Exomes 𝑓: 0.20 (756 hom.)
• Consequence: SNTB2 ENST00000336278.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

Genes affected

SNTB2 (HGNC:11169): (syntrophin beta 2) Dystrophin is a large, rod-like cytoskeletal protein found at the inner surface of muscle fibers. Dystrophin is missing in Duchenne Muscular Dystrophy patients and is present in reduced amounts in Becker Muscular Dystrophy patients. The protein encoded by this gene is a peripheral membrane protein found associated with dystrophin and dystrophin-related proteins. This gene is a member of the syntrophin gene family, which contains at least two other structurally-related genes. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNTB2	NM_006750.4	c.*65dup		3_prime_UTR_variant	7/7	ENST00000336278.9	NP_006741.1
SNTB2	NR_172088.1	n.1777dup		non_coding_transcript_exon_variant	8/8
SNTB2	NR_172089.1	n.1678dup		non_coding_transcript_exon_variant	7/7
SNTB2	NR_172090.1	n.1480dup		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNTB2	ENST00000336278.9	c.*65dup		3_prime_UTR_variant	7/7	1	NM_006750.4	ENSP00000338191	P1
SNTB2	ENST00000467311.5			3_prime_UTR_variant, NMD_transcript_variant	6/6	1		ENSP00000436443

Frequencies

GnomAD3 genomes AF: 0.156 AC: 22338 AN: 142764 Hom.: 1802 Cov.: 29

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0292

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.230

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.199 AC: 139612 AN: 701820 Hom.: 756 Cov.: 6 AF XY: 0.198 AC XY: 71481 AN XY: 360706

Gnomad4 AFR exome AF: 0.179

Gnomad4 AMR exome AF: 0.151

Gnomad4 ASJ exome AF: 0.205

Gnomad4 EAS exome AF: 0.118

Gnomad4 SAS exome AF: 0.160

Gnomad4 FIN exome AF: 0.182

Gnomad4 NFE exome AF: 0.210

Gnomad4 OTH exome AF: 0.206

GnomAD4 genome AF: 0.157 AC: 22352 AN: 142796 Hom.: 1803 Cov.: 29 AF XY: 0.154 AC XY: 10633 AN XY: 69074

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0295

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs34703750; hg19: chr16-69334880;