16-69307878-A-G

Position:

• chr16-69307878-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000336278.9(SNTB2):​c.*6954A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,132 control chromosomes in the GnomAD database, including 43,724 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.75 (43724 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SNTB2 ENST00000336278.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNTB2	NM_006750.4	c.*6954A>G		3_prime_UTR_variant	7/7	ENST00000336278.9	NP_006741.1
SNTB2	NR_172088.1	n.8666A>G		non_coding_transcript_exon_variant	8/8
SNTB2	NR_172089.1	n.8567A>G		non_coding_transcript_exon_variant	7/7
SNTB2	NR_172090.1	n.8369A>G		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNTB2	ENST00000336278.9	c.*6954A>G		3_prime_UTR_variant	7/7	1	NM_006750.4	ENSP00000338191	P1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113510 AN: 152014 Hom.: 43662 Cov.: 32

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.728

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.747 AC: 113630 AN: 152132 Hom.: 43724 Cov.: 32 AF XY: 0.745 AC XY: 55369 AN XY: 74340

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.732

Alfa AF: 0.684 Hom.: 48510

Bravo AF: 0.762

Asia WGS AF: 0.629 AC: 2187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.62

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: rs246129; hg19: chr16-69341781;