rs1541979

Positions:

• chr16-69291239-G-T

Variant summary

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

The NM_006750.4(SNTB2):​c.1345+6995G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,810 control chromosomes in the GnomAD database, including 9,075 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 0.33 (9075 hom., cov: 31)
• Consequence: SNTB2 NM_006750.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNTB2	NM_006750.4	c.1345+6995G>T		intron_variant		ENST00000336278.9
SNTB2	NR_172088.1	n.1434+6995G>T		intron_variant, non_coding_transcript_variant
SNTB2	NR_172089.1	n.1335+6995G>T		intron_variant, non_coding_transcript_variant
SNTB2	NR_172090.1	n.1137+6995G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNTB2	ENST00000336278.9	c.1345+6995G>T		intron_variant		1	NM_006750.4	P1
SNTB2	ENST00000467311.5	c.*330+6995G>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50619 AN: 151694 Hom.: 9036 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0982

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.327

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.334 AC: 50712 AN: 151810 Hom.: 9075 Cov.: 31 AF XY: 0.329 AC XY: 24415 AN XY: 74202

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.0985

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.336

Alfa AF: 0.327 Hom.: 1241

Bravo AF: 0.338

Asia WGS AF: 0.267 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.68

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: rs1541979; hg19: chr16-69325142;