rs71148989

Variant names:

• chr16-69300977-C-CAA
• rs34703750
• NM_006750.4:c.*64_*65dupAA

Your query was ambiguous. Multiple possible variants found:

• chr16-69300977-C-CAA
• chr16-69300977-C-CAAA
• chr16-69300977-CAA-C
• chr16-69300977-CAAAA-C
• chr16-69300977-CA-C
• chr16-69300977-C-CA

Variant summary

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

The NM_006750.4(SNTB2):​c.*64_*65dupAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00341 in 881,324 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00013 (0 hom., cov: 29)
  • Exomes 𝑓: 0.0040 (0 hom.)
• Consequence: SNTB2 NM_006750.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

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: Variant has high frequency in the MID (0.00453) population. However there is too low homozygotes in high coverage region: (expected more than 2, got 0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNTB2	NM_006750.4	c.*64_*65dupAA		3_prime_UTR_variant	Exon 7 of 7	ENST00000336278.9	NP_006741.1
SNTB2	NR_172088.1	n.1776_1777dupAA		non_coding_transcript_exon_variant	Exon 8 of 8
SNTB2	NR_172089.1	n.1677_1678dupAA		non_coding_transcript_exon_variant	Exon 7 of 7
SNTB2	NR_172090.1	n.1479_1480dupAA		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNTB2	ENST00000336278.9	c.*64_*65dupAA		3_prime_UTR_variant	Exon 7 of 7	1	NM_006750.4	ENSP00000338191.4
ENSG00000260914	ENST00000570054.3	c.93+1214_93+1215dupAA		intron_variant	Intron 1 of 9	5		ENSP00000461295.3

Frequencies

GnomAD3 genomes AF: 0.000133 AC: 19 AN: 142892 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000630

Gnomad ASJ AF: 0.00119

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000919

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00405 AC: 2989 AN: 738432 Hom.: 0 Cov.: 6 AF XY: 0.00410 AC XY: 1556 AN XY: 379950

Gnomad4 AFR exome AF: 0.00278 AC: 48 AN: 17242

Gnomad4 AMR exome AF: 0.00214 AC: 51 AN: 23822

Gnomad4 ASJ exome AF: 0.00502 AC: 87 AN: 17334

Gnomad4 EAS exome AF: 0.000661 AC: 19 AN: 28728

Gnomad4 SAS exome AF: 0.00214 AC: 119 AN: 55492

Gnomad4 FIN exome AF: 0.00213 AC: 83 AN: 39024

Gnomad4 NFE exome AF: 0.00469 AC: 2433 AN: 519116

Gnomad4 Remaining exome AF: 0.00383 AC: 130 AN: 33918

⚠️ The allele balance in gnomAD4 Exomes is highly skewed (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.000133 AC: 19 AN: 142892 Hom.: 0 Cov.: 29 AF XY: 0.000188 AC XY: 13 AN XY: 69098

Gnomad4 AFR AF: 0.00 AC: 0 AN: 0

Gnomad4 AMR AF: 0.000630 AC: 0.00063034 AN: 0.00063034

Gnomad4 ASJ AF: 0.00119 AC: 0.00119474 AN: 0.00119474

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00 AC: 0 AN: 0

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.0000919 AC: 0.0000919089 AN: 0.0000919089

Gnomad4 OTH AF: 0.00 AC: 0 AN: 0

Alfa AF: 0.00 Hom.: 58

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34703750; hg19: chr16-69334880;