rs6986718

Variant names:

• chr8-120623156-C-A
• rs6986718
• NM_021021.4:c.996+9288G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-120623156-C-A
• chr8-120623156-C-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.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
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.157 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTB1	NM_021021.4	MANE Select	c.996+9288G>T		intron	N/A	NP_066301.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTB1	ENST00000517992.2	TSL:1 MANE Select	c.996+9288G>T		intron	N/A	ENSP00000431124.1
	SNTB1	ENST00000519177.5	TSL:1	n.716+9288G>T		intron	N/A
	SNTB1	ENST00000395601.7	TSL:5	c.996+9288G>T		intron	N/A	ENSP00000378965.3

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

African (AFR) AF: 0.0679 AC: 2820 AN: 41548

American (AMR) AF: 0.0424 AC: 648 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3472

East Asian (EAS) AF: 0.160 AC: 829 AN: 5170

South Asian (SAS) AF: 0.167 AC: 805 AN: 4822

European-Finnish (FIN) AF: 0.0685 AC: 727 AN: 10616

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0612 AC: 4161 AN: 68034

Other (OTH) AF: 0.0595 AC: 126 AN: 2116

Alfa AF: 0.0664 Hom.: 370

Bravo AF: 0.0643

Asia WGS AF: 0.143 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.66
PhyloP100		-0.42
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: rs6986718; hg19: chr8-121635396;