NM_021021.4:c.788+11282G>T

Variant names:

• chr8-120682410-C-A
• rs11989782
• NM_021021.4:c.788+11282G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021021.4(SNTB1):​c.788+11282G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,176 control chromosomes in the GnomAD database, including 2,926 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 0.17 (2926 hom., cov: 32)
• Consequence: SNTB1 NM_021021.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNTB1	NM_021021.4	c.788+11282G>T		intron_variant	Intron 2 of 6	ENST00000517992.2	NP_066301.1
SNTB1	XM_011517239.3	c.788+11282G>T		intron_variant	Intron 2 of 4		XP_011515541.1
SNTB1	XM_047422126.1	c.209+11282G>T		intron_variant	Intron 2 of 6		XP_047278082.1
SNTB1	XM_047422127.1	c.209+11282G>T		intron_variant	Intron 2 of 6		XP_047278083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNTB1	ENST00000517992.2	c.788+11282G>T		intron_variant	Intron 2 of 6	1	NM_021021.4	ENSP00000431124.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26554 AN: 152058 Hom.: 2921 Cov.: 32

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0735

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.175 AC: 26574 AN: 152176 Hom.: 2926 Cov.: 32 AF XY: 0.172 AC XY: 12822 AN XY: 74388

African (AFR) AF: 0.0464 AC: 1928 AN: 41528

American (AMR) AF: 0.166 AC: 2537 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3472

East Asian (EAS) AF: 0.0745 AC: 386 AN: 5184

South Asian (SAS) AF: 0.120 AC: 577 AN: 4828

European-Finnish (FIN) AF: 0.275 AC: 2902 AN: 10566

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16583 AN: 67990

Other (OTH) AF: 0.193 AC: 407 AN: 2108

Alfa AF: 0.211 Hom.: 6690

Bravo AF: 0.163

Asia WGS AF: 0.146 AC: 505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		0.26
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: rs11989782; hg19: chr8-121694650;