rs6469937

Positions:

• chr8-120598198-G-A

Variant summary

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

The NM_021021.4(SNTB1):​c.997-22973C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,880 control chromosomes in the GnomAD database, including 19,933 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 0.48 (19933 hom., cov: 31)
• Consequence: SNTB1 NM_021021.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691

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]

SNTB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNTB1	NM_021021.4	c.997-22973C>T		intron_variant		ENST00000517992.2	NP_066301.1
SNTB1	XM_011517239.3	c.997-22973C>T		intron_variant			XP_011515541.1
SNTB1	XM_047422126.1	c.418-22973C>T		intron_variant			XP_047278082.1
SNTB1	XM_047422127.1	c.418-22973C>T		intron_variant			XP_047278083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNTB1	ENST00000517992.2	c.997-22973C>T		intron_variant		1	NM_021021.4	ENSP00000431124.1
SNTB1	ENST00000519177.5	n.717-22973C>T		intron_variant		1
SNTB1	ENST00000395601.7	c.997-22973C>T		intron_variant		5		ENSP00000378965.3
SNTB1	ENST00000648490.1	n.997-22973C>T		intron_variant				ENSP00000497707.1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72839 AN: 151762 Hom.: 19934 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.480 AC: 72856 AN: 151880 Hom.: 19933 Cov.: 31 AF XY: 0.475 AC XY: 35236 AN XY: 74204

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.497

Alfa AF: 0.580 Hom.: 13298

Bravo AF: 0.463

Asia WGS AF: 0.336 AC: 1167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.73

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: rs6469937; hg19: chr8-121610438;