16-69300977-CAAAA-CAAAAA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_006750.4(SNTB2):​c.*65dupA 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 NM_006750.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006750.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTB2	NM_006750.4	MANE Select	c.*65dupA		3_prime_UTR	Exon 7 of 7	NP_006741.1	Q13425-1
	SNTB2	NR_172088.1		n.1777dupA		non_coding_transcript_exon	Exon 8 of 8
	SNTB2	NR_172089.1		n.1678dupA		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTB2	ENST00000336278.9	TSL:1 MANE Select	c.*65dupA		3_prime_UTR	Exon 7 of 7	ENSP00000338191.4	Q13425-1
	ENSG00000260914	ENST00000570054.3	TSL:5	c.93+1215dupA		intron	N/A	ENSP00000461295.3	I3L4J1
	SNTB2	ENST00000958019.1		c.*65dupA		3_prime_UTR	Exon 7 of 7	ENSP00000628078.1

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

African (AFR) AF: 0.179 AC: 2897 AN: 16162

American (AMR) AF: 0.151 AC: 3332 AN: 22104

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 3363 AN: 16396

East Asian (EAS) AF: 0.118 AC: 3003 AN: 25480

South Asian (SAS) AF: 0.160 AC: 8308 AN: 51918

European-Finnish (FIN) AF: 0.182 AC: 6645 AN: 36418

Middle Eastern (MID) AF: 0.260 AC: 942 AN: 3624

European-Non Finnish (NFE) AF: 0.210 AC: 104502 AN: 497546

Other (OTH) AF: 0.206 AC: 6620 AN: 32172

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

African (AFR) AF: 0.130 AC: 5068 AN: 38916

American (AMR) AF: 0.145 AC: 2067 AN: 14286

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 563 AN: 3344

East Asian (EAS) AF: 0.0295 AC: 145 AN: 4916

South Asian (SAS) AF: 0.113 AC: 508 AN: 4502

European-Finnish (FIN) AF: 0.146 AC: 1244 AN: 8516

Middle Eastern (MID) AF: 0.230 AC: 63 AN: 274

European-Non Finnish (NFE) AF: 0.188 AC: 12248 AN: 65216

Other (OTH) AF: 0.183 AC: 358 AN: 1952

Alfa AF: 0.0443 Hom.: 58

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34703750; hg19: chr16-69334880; COSMIC: COSV60348275;