rs10875934

Variant names:

• chr12-49208422-A-G
• rs10875934
• ENST00000549554.1:n.491-410A>G

Variant summary

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

The ENST00000549554.1(TUBA1C):​n.491-410A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,126 control chromosomes in the GnomAD database, including 5,493 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 0.25 (5493 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: TUBA1C ENST00000549554.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 8 publications found

Genes affected

TUBA1C (HGNC:20768): (tubulin alpha 1c) Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Located in microtubule cytoskeleton and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549554.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TUBA1C	ENST00000549554.1	TSL:3	n.491-410A>G		intron	N/A
	TUBA1C	ENST00000550574.1	TSL:4	n.-124A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37570 AN: 152010 Hom.: 5490 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.247 AC: 37593 AN: 152126 Hom.: 5493 Cov.: 32 AF XY: 0.254 AC XY: 18918 AN XY: 74358

African (AFR) AF: 0.174 AC: 7216 AN: 41520

American (AMR) AF: 0.257 AC: 3928 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 605 AN: 3466

East Asian (EAS) AF: 0.718 AC: 3713 AN: 5170

South Asian (SAS) AF: 0.433 AC: 2091 AN: 4824

European-Finnish (FIN) AF: 0.302 AC: 3188 AN: 10572

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16176 AN: 67994

Other (OTH) AF: 0.232 AC: 489 AN: 2112

Alfa AF: 0.240 Hom.: 14774

Bravo AF: 0.240

Asia WGS AF: 0.535 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.43
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10875934; hg19: chr12-49602205;