16-69300977-CA-C

Variant names:

• chr16-69300977-CA-C
• rs34703750
• NM_006750.4:c.*65delA

Variant summary

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

The NM_006750.4(SNTB2):​c.*65delA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 799,440 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 0.0012 (0 hom., cov: 29)
  • Exomes 𝑓: 0.12 (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 Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNTB2	NM_006750.4	c.*65delA		3_prime_UTR_variant	Exon 7 of 7	ENST00000336278.9	NP_006741.1
SNTB2	NR_172088.1	n.1777delA		non_coding_transcript_exon_variant	Exon 8 of 8
SNTB2	NR_172089.1	n.1678delA		non_coding_transcript_exon_variant	Exon 7 of 7
SNTB2	NR_172090.1	n.1480delA		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNTB2	ENST00000336278.9	c.*65delA		3_prime_UTR_variant	Exon 7 of 7	1	NM_006750.4	ENSP00000338191.4
ENSG00000260914	ENST00000570054.3	c.93+1215delA		intron_variant	Intron 1 of 9	5		ENSP00000461295.3

Frequencies

GnomAD3 genomes AF: 0.00123 AC: 175 AN: 142608 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.000515

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00119

Gnomad ASJ AF: 0.000299

Gnomad EAS AF: 0.000811

Gnomad SAS AF: 0.000442

Gnomad FIN AF: 0.00841

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000890

Gnomad OTH AF: 0.00103

GnomAD4 exome AF: 0.115 AC: 75786 AN: 656800 Hom.: 0 Cov.: 6 AF XY: 0.118 AC XY: 39779 AN XY: 336084

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.173

Gnomad4 ASJ exome AF: 0.141

Gnomad4 EAS exome AF: 0.175

Gnomad4 SAS exome AF: 0.172

Gnomad4 FIN exome AF: 0.131

Gnomad4 NFE exome AF: 0.103

Gnomad4 OTH exome AF: 0.122

GnomAD4 genome AF: 0.00122 AC: 174 AN: 142640 Hom.: 0 Cov.: 29 AF XY: 0.00128 AC XY: 88 AN XY: 68974

Gnomad4 AFR AF: 0.000514

Gnomad4 AMR AF: 0.00119

Gnomad4 ASJ AF: 0.000299

Gnomad4 EAS AF: 0.000610

Gnomad4 SAS AF: 0.000444

Gnomad4 FIN AF: 0.00841

Gnomad4 NFE AF: 0.000890

Gnomad4 OTH AF: 0.00103

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;