rs10090787

Variant names:

• chr8-120798309-C-T
• rs10090787
• NM_021021.4:c.571+12964G>A

Variant summary

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

The NM_021021.4(SNTB1):​c.571+12964G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,792 control chromosomes in the GnomAD database, including 9,253 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (★).

• Frequency: Genomes: 𝑓 0.34 (9253 hom., cov: 32)
• Consequence: SNTB1 NM_021021.4 intron
• Clinical Significance: association criteria provided, single submitter O:1
• Conservation: PhyloP100: -1.32
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021021.4. 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
	SNTB1	NM_021021.4	MANE Select	c.571+12964G>A		intron	N/A	NP_066301.1	Q13884-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTB1	ENST00000517992.2	TSL:1 MANE Select	c.571+12964G>A		intron	N/A	ENSP00000431124.1	Q13884-1
	SNTB1	ENST00000519177.5	TSL:1	n.291+12964G>A		intron	N/A
	SNTB1	ENST00000395601.7	TSL:5	c.571+12964G>A		intron	N/A	ENSP00000378965.3	Q13884-1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51551 AN: 151674 Hom.: 9228 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.340 AC: 51629 AN: 151792 Hom.: 9253 Cov.: 32 AF XY: 0.340 AC XY: 25241 AN XY: 74196

African (AFR) AF: 0.442 AC: 18292 AN: 41356

American (AMR) AF: 0.291 AC: 4433 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 983 AN: 3468

East Asian (EAS) AF: 0.116 AC: 597 AN: 5152

South Asian (SAS) AF: 0.327 AC: 1574 AN: 4818

European-Finnish (FIN) AF: 0.362 AC: 3827 AN: 10586

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20646 AN: 67878

Other (OTH) AF: 0.335 AC: 702 AN: 2096

Alfa AF: 0.320 Hom.: 14415

Bravo AF: 0.337

Asia WGS AF: 0.272 AC: 947 AN: 3478

ClinVar

ClinVar submissions

Significance: association

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	-	Lip and oral cavity carcinoma (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.17
PhyloP100		-1.3
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: rs10090787; hg19: chr8-121810549;