rs10717744

Variant names:

• chr6-3224590-GAA-G
• rs10717744
• NM_178012.5:c.*159_*160delTT

Your query was ambiguous. Multiple possible variants found:

• chr6-3224590-GAA-G
• chr6-3224590-GAA-GA
• chr6-3224590-GAA-GAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_178012.5(TUBB2B):​c.*159_*160delTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 1,062,708 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00053 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00015 (0 hom.)
• Consequence: TUBB2B NM_178012.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

Genes affected

TUBB2B (HGNC:30829): (tubulin beta 2B class IIb) The protein encoded by this gene is a beta isoform of tubulin, which binds GTP and is a major component of microtubules. This gene is highly similar to TUBB2A and TUBB2C. Defects in this gene are a cause of asymmetric polymicrogyria. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000526 (80/152114) while in subpopulation AFR AF= 0.00166 (69/41476). AF 95% confidence interval is 0.00135. There are 1 homozygotes in gnomad4. There are 42 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 80 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBB2B	NM_178012.5	c.*159_*160delTT		3_prime_UTR_variant	Exon 4 of 4	ENST00000259818.8	NP_821080.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBB2B	ENST00000259818	c.*159_*160delTT		3_prime_UTR_variant	Exon 4 of 4	1	NM_178012.5	ENSP00000259818.6

Frequencies

GnomAD3 genomes AF: 0.000526 AC: 80 AN: 151996 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000393

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.000480

GnomAD4 exome AF: 0.000150 AC: 137 AN: 910594 Hom.: 0 AF XY: 0.000143 AC XY: 65 AN XY: 453634

Gnomad4 AFR exome AF: 0.00157

Gnomad4 AMR exome AF: 0.000253

Gnomad4 ASJ exome AF: 0.0000601

Gnomad4 EAS exome AF: 0.0000302

Gnomad4 SAS exome AF: 0.0000721

Gnomad4 FIN exome AF: 0.000114

Gnomad4 NFE exome AF: 0.000115

Gnomad4 OTH exome AF: 0.000220

GnomAD4 genome AF: 0.000526 AC: 80 AN: 152114 Hom.: 1 Cov.: 0 AF XY: 0.000565 AC XY: 42 AN XY: 74358

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.000393

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.000475

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs10717744; hg19: chr6-3224824;