chr8-120571043-A-G

Variant names:

• chr8-120571043-A-G
• rs4455882
• ENST00000519177.5:n.1178T>C

Variant summary

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

The ENST00000519177.5(SNTB1):​n.1178T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 439,396 control chromosomes in the GnomAD database, including 74,923 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 0.46 (18596 hom., cov: 32)
  • Exomes 𝑓: 0.61 (56327 hom.)
• Consequence: SNTB1 ENST00000519177.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 13 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=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519177.5. 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.1136+4043T>C		intron	N/A	NP_066301.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTB1	ENST00000519177.5	TSL:1	n.1178T>C		non_coding_transcript_exon	Exon 5 of 5
	SNTB1	ENST00000517992.2	TSL:1 MANE Select	c.1136+4043T>C		intron	N/A	ENSP00000431124.1
	SNTB1	ENST00000395601.7	TSL:5	c.1136+4043T>C		intron	N/A	ENSP00000378965.3

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70070 AN: 151954 Hom.: 18591 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.614 AC: 176519 AN: 287324 Hom.: 56327 Cov.: 5 AF XY: 0.607 AC XY: 88133 AN XY: 145152

African (AFR) AF: 0.210 AC: 1254 AN: 5970

American (AMR) AF: 0.472 AC: 3424 AN: 7248

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 2037 AN: 3860

East Asian (EAS) AF: 0.232 AC: 1682 AN: 7262

South Asian (SAS) AF: 0.455 AC: 11525 AN: 25326

European-Finnish (FIN) AF: 0.608 AC: 3841 AN: 6314

Middle Eastern (MID) AF: 0.537 AC: 421 AN: 784

European-Non Finnish (NFE) AF: 0.665 AC: 145676 AN: 218950

Other (OTH) AF: 0.574 AC: 6659 AN: 11610

GnomAD4 genome AF: 0.461 AC: 70105 AN: 152072 Hom.: 18596 Cov.: 32 AF XY: 0.458 AC XY: 34047 AN XY: 74322

African (AFR) AF: 0.205 AC: 8515 AN: 41460

American (AMR) AF: 0.449 AC: 6859 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1675 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1285 AN: 5164

South Asian (SAS) AF: 0.421 AC: 2029 AN: 4822

European-Finnish (FIN) AF: 0.584 AC: 6178 AN: 10586

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41881 AN: 67986

Other (OTH) AF: 0.489 AC: 1030 AN: 2106

Alfa AF: 0.534 Hom.: 45691

Bravo AF: 0.443

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.5
DANN	Benign	0.91
PhyloP100		0.075
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: rs4455882; hg19: chr8-121583283;