rs34703750

Variant names:

• chr16-69300977-CAAAA-C
• rs34703750
• NM_006750.4:c.*62_*65delAAAA

Your query was ambiguous. Multiple possible variants found:

• chr16-69300977-CAAAA-C
• chr16-69300977-CAAAA-CA
• chr16-69300977-CAAAA-CAA
• chr16-69300977-CAAAA-CAAA
• chr16-69300977-CAAAA-CAAAAA
• chr16-69300977-CAAAA-CAAAAAA
• chr16-69300977-CAAAA-CAAAAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_006750.4(SNTB2):​c.*62_*65delAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SNTB2 NM_006750.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 1 publications found

Genes affected

SNTB2 (HGNC:11169): (syntrophin beta 2) 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]

ENSG00000260914 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006750.4. 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
	SNTB2	NM_006750.4	MANE Select	c.*62_*65delAAAA		3_prime_UTR	Exon 7 of 7	NP_006741.1	Q13425-1
	SNTB2	NR_172088.1		n.1774_1777delAAAA		non_coding_transcript_exon	Exon 8 of 8
	SNTB2	NR_172089.1		n.1675_1678delAAAA		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTB2	ENST00000336278.9	TSL:1 MANE Select	c.*62_*65delAAAA		3_prime_UTR	Exon 7 of 7	ENSP00000338191.4	Q13425-1
	ENSG00000260914	ENST00000570054.3	TSL:5	c.93+1212_93+1215delAAAA		intron	N/A	ENSP00000461295.3	I3L4J1
	SNTB2	ENST00000958019.1		c.*62_*65delAAAA		3_prime_UTR	Exon 7 of 7	ENSP00000628078.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 742150 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 381906

African (AFR) AF: 0.00 AC: 0 AN: 17310

American (AMR) AF: 0.00 AC: 0 AN: 23920

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17444

East Asian (EAS) AF: 0.00 AC: 0 AN: 28826

South Asian (SAS) AF: 0.00 AC: 0 AN: 55760

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39210

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3774

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 521806

Other (OTH) AF: 0.00 AC: 0 AN: 34100

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 58

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.8

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: rs34703750; hg19: chr16-69334880;