16-69300977-C-CAA

Position:

• chr16-69300977-C-CAA

Variant summary

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

The NM_006750.4(SNTB2):​c.*64_*65dupAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00341 in 881,324 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 0.00013 (0 hom., cov: 29)
  • Exomes 𝑓: 0.0040 (0 hom.)
• Consequence: SNTB2 NM_006750.4 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]

ENSG00000260914 (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
SNTB2	NM_006750.4	c.*64_*65dupAA		3_prime_UTR_variant	7/7	ENST00000336278.9	NP_006741.1
SNTB2	NR_172088.1	n.1776_1777dupAA		non_coding_transcript_exon_variant	8/8
SNTB2	NR_172089.1	n.1677_1678dupAA		non_coding_transcript_exon_variant	7/7
SNTB2	NR_172090.1	n.1479_1480dupAA		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_*65dupAA		3_prime_UTR_variant	7/7	1	NM_006750.4	ENSP00000338191.4
ENSG00000260914	ENST00000570054.3	c.93+1214_93+1215dupAA		intron_variant		5		ENSP00000461295.3

Frequencies

GnomAD3 genomes AF: 0.000133 AC: 19 AN: 142892 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000630

Gnomad ASJ AF: 0.00119

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000919

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00405 AC: 2989 AN: 738432 Hom.: 0 Cov.: 6 AF XY: 0.00410 AC XY: 1556 AN XY: 379950

Gnomad4 AFR exome AF: 0.00278

Gnomad4 AMR exome AF: 0.00214

Gnomad4 ASJ exome AF: 0.00502

Gnomad4 EAS exome AF: 0.000661

Gnomad4 SAS exome AF: 0.00214

Gnomad4 FIN exome AF: 0.00213

Gnomad4 NFE exome AF: 0.00469

Gnomad4 OTH exome AF: 0.00383

GnomAD4 genome AF: 0.000133 AC: 19 AN: 142892 Hom.: 0 Cov.: 29 AF XY: 0.000188 AC XY: 13 AN XY: 69098

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000630

Gnomad4 ASJ AF: 0.00119

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000919

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;