Genetic Variant SNTB2:c.*6954A>G (chr16-69307878-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006750.4(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
NM_006750.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.478

Publications

17 publications found

Variant links:

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]

SNTB2 links:

ENSG00000260914 (HGNC:):

ENSG00000260914 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	MANE	Protein	UniProt
SNTB2	NM_006750.4 link	c.*6954A>G	3_prime_UTR_variant	Exon 7 of 7	ENST00000336278.9	NP_006741.1	Q13425-1A0A024R732
SNTB2	NR_172088.1 link	n.8666A>G	non_coding_transcript_exon_variant	Exon 8 of 8
SNTB2	NR_172089.1 link	n.8567A>G	non_coding_transcript_exon_variant	Exon 7 of 7
SNTB2	NR_172090.1 link	n.8369A>G	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 link	c.*6954A>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_006750.4	ENSP00000338191.4		Q13425-1
ENSG00000260914	ENST00000570054.3 link	c.93+8104A>G		intron_variant	Intron 1 of 9	5		ENSP00000461295.3		I3L4J1

Frequencies

GnomAD3 genomes

AF:

0.747

AC:

113510

AN:

152014

Hom.:

43662

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.747

AC:

113630

AN:

152132

Hom.:

43724

Cov.:

AF XY:

0.745

AC XY:

55369

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.939

AC:

39017

AN:

41542

American (AMR)

AF:

0.749

AC:

11448

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.561

AC:

1946

AN:

3470

East Asian (EAS)

AF:

0.509

AC:

2634

AN:

5174

South Asian (SAS)

AF:

0.687

AC:

3309

AN:

4816

European-Finnish (FIN)

AF:

0.671

AC:

7084

AN:

10554

Middle Eastern (MID)

AF:

0.724

AC:

213

AN:

294

European-Non Finnish (NFE)

AF:

0.673

AC:

45750

AN:

67976

Other (OTH)

AF:

0.732

AC:

1544

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1382

2764

4146

5528

6910

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

840

1680

2520

3360

4200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.693

Hom.:

62932

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

(source)

DANN

Benign

0.62

PhyloP100

-0.48

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over