rs6986718

chr8-120623156-C-Achr8-120623156-C-T

Variant summary

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

The NM_021021.4(SNTB1):c.996+9288G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,278 control chromosomes in the GnomAD database, including 421 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 0.068 (421 hom., cov: 33)
• Consequence: SNTB1 NM_021021.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

Genes affected

SNTB1 (HGNC:11168): (syntrophin beta 1) 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNTB1	NM_021021.4	c.996+9288G>T		intron_variant		ENST00000517992.2
SNTB1	XM_011517239.3	c.996+9288G>T		intron_variant
SNTB1	XM_047422126.1	c.417+9288G>T		intron_variant
SNTB1	XM_047422127.1	c.417+9288G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNTB1	ENST00000517992.2	c.996+9288G>T		intron_variant		1	NM_021021.4	P1
SNTB1	ENST00000519177.5	n.716+9288G>T		intron_variant, non_coding_transcript_variant		1
SNTB1	ENST00000395601.7	c.996+9288G>T		intron_variant		5		P1
SNTB1	ENST00000648490.1	c.996+9288G>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0677 AC: 10295 AN: 152160 Hom.: 423 Cov.: 33

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0677 AC: 10302 AN: 152278 Hom.: 421 Cov.: 33 AF XY: 0.0694 AC XY: 5167 AN XY: 74448

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.0424

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0612

Gnomad4 OTH AF: 0.0595

Alfa AF: 0.0674 Hom.: 218

Bravo AF: 0.0643

Asia WGS AF: 0.143 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.6
Dann	Benign	0.66

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: rs6986718; hg19: chr8-121635396;