chr16-69291239-G-T

Variant names:

• chr16-69291239-G-T
• rs1541979
• NM_006750.4:c.1345+6995G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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.1345+6995G>T		intron	N/A	NP_006741.1	Q13425-1
	SNTB2	NR_172088.1		n.1434+6995G>T		intron	N/A
	SNTB2	NR_172089.1		n.1335+6995G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTB2	ENST00000336278.9	TSL:1 MANE Select	c.1345+6995G>T		intron	N/A	ENSP00000338191.4	Q13425-1
	SNTB2	ENST00000467311.5	TSL:1	n.*330+6995G>T		intron	N/A	ENSP00000436443.1	Q13425-2
	SNTB2	ENST00000958019.1		c.1315+6995G>T		intron	N/A	ENSP00000628078.1

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

African (AFR) AF: 0.450 AC: 18604 AN: 41360

American (AMR) AF: 0.273 AC: 4151 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3472

East Asian (EAS) AF: 0.0985 AC: 509 AN: 5170

South Asian (SAS) AF: 0.298 AC: 1435 AN: 4812

European-Finnish (FIN) AF: 0.263 AC: 2778 AN: 10546

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.313 AC: 21233 AN: 67920

Other (OTH) AF: 0.336 AC: 710 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.68
PhyloP100		-0.67
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: rs1541979; hg19: chr16-69325142;