16-69300977-CAA-C

Position:

• chr16-69300977-CAA-C

Variant summary

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

The ENST00000336278.9(SNTB2):​c.*64_*65del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 876,360 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000070 (0 hom., cov: 29)
  • Exomes 𝑓: 0.0013 (0 hom.)
• Consequence: SNTB2 ENST00000336278.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

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 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
SNTB2	NM_006750.4	c.*64_*65del		3_prime_UTR_variant	7/7	ENST00000336278.9	NP_006741.1
SNTB2	NR_172088.1	n.1776_1777del		non_coding_transcript_exon_variant	8/8
SNTB2	NR_172089.1	n.1677_1678del		non_coding_transcript_exon_variant	7/7
SNTB2	NR_172090.1	n.1479_1480del		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNTB2	ENST00000336278.9	c.*64_*65del		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: 0.00000700 AC: 1 AN: 142850 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000117

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00125 AC: 917 AN: 733510 Hom.: 0 AF XY: 0.00118 AC XY: 445 AN XY: 377152

Gnomad4 AFR exome AF: 0.000585

Gnomad4 AMR exome AF: 0.00123

Gnomad4 ASJ exome AF: 0.000990

Gnomad4 EAS exome AF: 0.000776

Gnomad4 SAS exome AF: 0.00140

Gnomad4 FIN exome AF: 0.00150

Gnomad4 NFE exome AF: 0.00129

Gnomad4 OTH exome AF: 0.00104

GnomAD4 genome AF: 0.00000700 AC: 1 AN: 142850 Hom.: 0 Cov.: 29 AF XY: 0.0000145 AC XY: 1 AN XY: 69078

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000117

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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;